This post reports a new form of life that is clearly a member of the archaea, with characteristics of that group, but also lacking a vital feature of other archaea as well as other bacteria and all eukaryotes: metabolism: the pathways (mostly involving enzymatic proteins) that keep an organism going and reproducing by converting nutrients into energy. Its lack of genes for metabolism makes it resemble a virus, what hijacks its nutrients from the cells it infects. But viruses can’t completely self-replicate like this new critter, for viruses also partly hijack the DNA/RNA replication system of their hosts.

The new creature, whose appearance is unknown since it was identified from DNA alone, must get its metabolites through association with other species. Finally, the new creature does have something that viruses lack—a complete system for replicating its genome: ribosomes, DNA, genes for transfer RNAs, and so on. In other words, in important ways it’s different from viruses, but also different from other archaea as well as bacteria and eukaryotes (organisms with “true cells” that have their DNA in the nucleus and have membrane-covered organelles like mitochondria and chloroplasts).  The DNA of this creature is in a single circular chromosome like that of bacteria and archaea. Its unique features appears to make it a member of a new domain of life.

The question is this: is this new organism even alive? Viruses are regarded by many biologists as “not alive” because they can’t grow, they have no metabolism to sustain themselves, and are completely dependent for reproduction on the replication machinery of other organisms (bacteria or eukaryotes) they parasitize.

Well, read about this new organism below, discovered by sequencing DNA inside of a singe eukaryotic cell tell me if you think it’s “alive.”

But I’m getting ahead of myself. Let’s review:

There are three domains of life: the bacteria, the archaea (discovered only in 1977 by Woese and Fox), and the eukaryotes (everything else, all having membrane bound nuclei and organelles). Together, the bacteria and archaea are called “prokaryotes” (i.e., single celled microorganisms), and everything else besides viruses comprise the “eukaryotes.”

The phylogeny (family tree) of these domains is shown below.  It was realized only recently that all organisms with true cells (e.g., us) descended from archaea, as shown below. That means three things. First, we are more closely related to the archaea (which often live in weird places like hot springs or hyper-salty water) than we are to bacteria. Eukaryotes did not evolve from bacteria.

Second, eukaryotes like us could be thought of as archaea, since we are nested within that group. In the same way, we could be thought of as fish, and birds as reptiles.

Finally, archaea are considered paraphyletic: the group does not contain all the descendants of its common ancestor. The eukaryotes are not considered archaea, but ARE descendants of the common ancestor of archaea; they just branched off later into a new domain of life.

Now this family tree was constucted from DNA sequence similarity, but archaea also share certain traits with eukaryotes that bacteria don’t have, including “shared metabolic pathways, similar enzymes involved in transcription and translation, and DNA replication mechanisms.” That is what a query to Google tells me. Remember, this area is far from my own biological expertise, so if you see an error, let me know!

This tree is from Sadava et al. 2020. Life. The science of biology. 12th edition. Oxford Univ. Press)

Here is a comparison of the traits of the groups (there are overlaps),from Wikipedia.

Note that all three groups have metabolism (pathways to produce energy and grow), and cell walls, but eukaryotes have a special cell wall with two layers of lipids and a layer of protein. Viruses, not shown in this comparison, have only a protein capsule around them. (Bacteria and archaea have more complicated cell walls.)

Viruses do not metabolize and are widely regarded as “nonliving particles”.  Bacteria and most archaea have metabolism.

The paper describing the new finding is apparently not yet published, but you can find it at bioRχiv by clicking the title below or downlading the pdf here.

How did they find this thing? In a weird way. The researchers took a single individual of the dinoflagellate Citharistes regius and amplified and sequenced all the DNA it contained. Besides the DNA of the dinoflagellate, it also found DNA from three other types of organisms: cyanobacteria (photosynthetic bacteria once called “blue-green algae”), two species of gamma proteobacteria (a well-known group) and then the weird species under consideration, which they call Candidatus Sukunaarchaeum mirabile. This apparently means it’s a candidate species that hasn’t been formally described.  We’ll call it CSM in this post. We don’t know what it looks like or what its ecology and behavior is, except we know it must be parasitic, commensal, or symbiotic with some other species. It cannot live on its own because it can’t metabolize.

Here is its genome shown in the paper. This is all we know of the organism’s biology:

 

It is in the Archaea as the DNA certainly shows its affinity. But, as shown below, its lineage originated very soon after the archaea branched off from their common ancestor with bacteria.

It has a very small genome: 238,000 base pairs, though that is not the smallest genome known of any organism in the three domains of life (note I’m using “life” here, though this thing may be more virus-like and hence “not alive”).

The chomosome is circular, presumably because sequencing it, one arrives back at the beginning again.

It has 222 genes, most of which are devoted to the machinery for making copies of itself. These include transfer RNAs and ribosomal RNAs, which are not found in viruses, all of which hijack that stuff from the cells they infect.

It has NO genes for metabolism (no genes for it), so CSM must grow and divide using resources from cells that it hijacks. Other bacteria and archaea (and of course eukaryotes) have the genes for metabolic processes, making CSM more virus-like. But, as I said, it differs from viruses by having a complete set of “self-replication core machinery” and genes that are like those in archaea.

189 of its 222 genes make proteins. All but five of these are devoted to self-replication. Several are very large and strongly suggest that they constitute part of the cell wall (they call it “membrane”), though the researchers are not sure about this.

Here’s a summary of the organism. Note that its unique character, lacking metabolism, makes it distinct from other domains of archaean life.

 

And a figure from the paper  (just look at “a” on the left side) showing where it fits in the family tree of prokaryotes. It branches off from the rest of the archaea early, and then evolves very fast, as you can see by the long branch of its lineage, probably reflecting strong natural selection on the lineage.

To summarize:

CSM is an Archaea as seen from its DNA sequence.  Of this there is no doubt.

But unlike other Archaea or even bacteria, it has NO metabolic machinery. In this way it’s similar to a virus.

But it is dissimilar to viruses because it has the complete machinery for self-replicating its genome, which viruses lack.

Ergo, it must be associated in some way with other organisms to be able to replicate.

We have no idea what it looks like, though it almost certainly is a cell rather than a virus.

Here’s how the authors highlight CSM’s uniqueness:

The discovery of Sukunaarchaeum not only expands the known boundaries of archaeal diversity but also challenges fundamental concepts of cellular life. The extreme metabolic simplification raises fundamental questions about the minimal requirements for cellular life. Sukunaarchaeum, focused almost entirely on genetic self-perpetuation, represents a compelling example of how far metabolic reduction can proceed within a cellular framework. Its minimal genome, absolute host dependence necessitated by profound metaboliceduction, rapid evolution, and significant investment in large, membrane-associated proteins potentially mediating host interaction constitute a unique combination of characteristics that are collectively reminiscent of viruses. Nonetheless, Sukunaarchaeum remains fundamentally cellular – a key distinction from viruses, which typically lack their own core replication machinery genes and rely on host systems. It possesses ribosomes and the core transcriptional and translational apparatus inherited from cellular ancestors. Thus, while clearly cellular, its extreme metabolic dependence and specialization for self-replication are virus-like in nature, suggesting that Sukunaarchaeum may represent the closest cellular entity discovered to date that approaches a viral strategy of existence.

The authors found this organism by sequencing a single eukaryotic cell; CSM was likely inside this cell, like a virus in a human cell, but we don’t know if CSM damages its host(s) in any way. It is likely that many more organisms like this exist but aren’t known because people don’t do DNA sequencing of entire single-celled eukaryotes very often. Dinoflagellates are aquatic organisms, but there may be more stuff like CSM found by sequencing DNA in the soil.

I’ll add that this organism might give us an idea of how viruses originated because, if it loses some of its core replication machinery and genes for making membranes, it would become a virus. It is unlikely to be a virus that might develop into an archaean, as it already is an archaean with a membrane, but would have to evolve a tremendous amount of new metabolic machinery to be able to fuel itself, and that metabolic machinery would have to be genetically similar to the metabolic machinery of already-existing archaea.  That would be an unheard-of event of convergent evolution, thus very unlikely.  This thing, so far, is sui generis.

Finally, IS IT ALIVE? That, as you might guess, depends on your definition of “life”.

If you count the ability to self-replicate on its own, CSM is alive. In that sense viruses are not alive, and most of us think they’re not. (Bur remember that it needs to be assocated with another species to self-replicate.)

But if you count the ability to sustain itself by metabolizing and fueling its own replication, then it is NOT alive.

You pays your money, you takes your choice.

Who hasn’t heard the statement, “Live each day as if it were your last.”?   I take this to mean that one should live in such a way that, on your deathbed, you would have minimal regrets. (Granted, determinism rules how we live our lives, but we can certainly be influenced in our behavior by statements like these.)

Now people will vary in what they consider “their fullest life.” Some would want to devote more time to their family or friends, others to books, still others to social causes, and some (like me) to more travel—to seeing the richness of the world before I leave it forever. Although few of us would want to change places with present or historical figures, I suspect that most of us would like to be more like “behavioral role models”—that is, living in a way that maximizes the use of our time.

And, while pondering my mortality this morning (don’t worry, if you’re young you’ll get there eventually!), as well as my obsession with work to the detriment of fun, I thought about which people in history I would judge as having lived the fullest life. I couldn’t think of just one person, but I have a list of several people whose lives seemed very full to me.

The first two people combine both aspects of what for me would be a full life: action for a good cause and scholarship (best combined with writing).

T. E. Lawrence (“Lawrence of Arabia”). Fiercely smart and classically educated (he started life as an archaeologist, traveling 1000 miles on foot through the Middle East), Lawrence later allied himself with the Arabs against the Turks during WWI, becoming the famous “Lawrence of Arabia” of movie lore. He was also a great writer.  The downside, of course, is that he became somewhat of a recluse in later life, and was apparently asexual, cutting himself off from one of life’s great pleasures. Still, who can deny that the man had a full (though brief) life?

Winston Churchill. Also hugely smart, a great writer and speaker (he won a Nobel Prize for Literature), and a man of action (read about his early life as a soldier in Manchester’s great biography), Churchill surely lived a full life, capped by helping save Britain from the Nazis during World War II. He loved food and drink, and he loved to paint.  As far as I can see, Churchill wasted very little time.

Neal Cassady. Best known as the model for “Dean Moriarty” in Kerouac’s On the Road and as the driver of the “Furthur” bus in Tom Wolfe’s Electric Kool-Aid Acid Test,  Cassady wasn’t a scholar, but his few letters show that he could write well, if intensely. More important, he is the one real person I name who really did live every day as if it were his last. He didn’t think ahead and he didn’t worry. He did what he liked to do: hang around with fellow beats, have sex, drink, and drive.  I wouldn’t want to be him, not with all the drugs and booze, but I could use a bit of his view of life.

Anthony Bourdain. This choice was problematic as Bourdain had a rough early life, was addicted to drugs when younger, and was a depressive, ultimately killing himself at 61. On the other hand, he got paid to travel the world to eat, immersing himself in the diversity of cultures, and made tons of friends everywhere.  He was, of course also a good writer. His life may not have been a bed of roses, but it was a full life.

Zorba the Greek. Alexis Zorba was of course a fictional character, but his portrayal in the eponymous novel written by Kazantzakis shows a man who threw himself completely into life, whether it be sniffing a lemon, working in a lignite mine, playing his santouri, or romancing the ladies.  This book still inspires me even if I fail to live up to Zorba’s standards (he’d consider me a “scribbler”, like the writer in the book).  His death is memorable: he’s living with a 25 year old woman, even though he’s quite old, and asks the schoolmaster to write to the “scribbler” (inviting him to come and get his santouri), whom Zorba hasn’t seen in years. His girlfriend writes the following in a letter sent to the scribbler:

“Come here, schoolmaster,” he said. “I have a friend in Greece. When I am dead write to him and tell him that right until the very last minute I was in full possession of my senses and was thinking of him. And tell him that whatever I have done, I have no regrets. Tell him I hope he is well and that it’s about time he showed a bit of sense.

“Listen, just another minute. If some priest or other comes to take my confession and give me the sacrament, tell him to clear out, quick, and leave me his curse instead! I’ve done heaps and heaps of things in my life, but I still did not do enough. Men like me ought to live a thousand years. Good night!”

Of course this is to invite you to share your own role models for life, if you have any, or weigh in on mine. For those readers who say they have no such models because their own lives are already full, I envy you!