Here Are My Bacterial Tools, Use Them Wisely
Thus said the mitochondria to the future eukaryotic cell
If mitochondria could talk, I would imagine them having a voice similar to Master Yoda’s.
The same goes for the syntax.
Yoda is a powerful Jedi. He can harness the power of the force. He was assigned to Luke Skywalker.
Despite his skill and ability, Luke Skywalker was bigger than him. Luke had a lot to learn and gain from Yoda. It didn’t turn out well, but it was somewhat necessary to create an adversary worthy of Anakin Skywalker — Luke Skywalker’s son.
Yoda believed Anakin to be the chosen one. So he trained him to his final breath before being united with The Force. In a different world, I can imagine what he would have said to Anakin:
My tools, here they are. Wisely, use them. Guide you, I shall. As I will be one with the force, trust it, you must.
Hopefully, the mitochondria would have better syntax. Before submitting (not dying) to its large host, it would have confessed something similar:
Here are my bacterial tools. Use them wisely.
It would then commit to shedding most of its genes to the nucleus of its host. Most of the non-essential genes. It would shed too much genetic component, it would no longer be able to survive independently outside its host.
The bacterial endosymbionts have the smallest genomes. At a measly 160kb, Carsonella ruddii has the smallest genome. It is the endosymbiont of psyllids, plant-feeding insects. It’s also an obligate symbiont, meaning it cannot survive independently outside the host, like mitochondria.
Over 99% of mitochondrial genes have moved to the nucleus. Why did the 1% remain?
Perhaps the most important lesson to derive from these pieces of evidence is that genes are not what the gene-centred view of evolution purports. This view of evolution considers organisms as vehicles and genes as the masters of these vehicles. How then are the masters shed from their own cars?
To answer these questions, we need to revisit another group of cells, the most dominant cells in all mammalian species.
The red blood cells
When you blush, get hit in the nose, sprain your ankle, or cut your finger, the redness underneath your skin or from a broken skin surface reflects the inevitable — blood.
It’s red because of haemoglobin, the active component inside red blood cells. It’s exaggerated because of the mediators of inflammation. Mostly.
In vertebrates, mammals have the purest red blood cells. It’s enucleated. That means they lack a nucleus (in normal circumstances, as certain disease states preserve a significant proportion of red blood cells with nuclei).
A mature and healthy red blood cell extrudes its nucleus to create more room for haemoglobin, the complex molecule responsible for transporting oxygen. Why should a cell remove not just the genome, but the house of the genome? Isn’t that throwing away the baby with the bathwater, plus the basin? This is not usually the case in other vertebrates such as fishes, amphibians, and reptiles.
Without a nucleus, the red blood cell takes a biconcave shape. It further increases the surface area to carry more oxygen inside the haemoglobin, which is known as oxygen saturation. During COVID-19, it was the vital sign used to screen for potential victims.
Why should a cell lose its complete genome? If the gene-centred view of evolution is correct, why should the entire genome be extruded?
The only reason I can think of is that the cell uses the genome as a toolset. The genes are the tools. These are the raw materials for making proteins. The energy required to make the tools (genetic replication) is less compared to what is needed to execute the work (protein metabolism).
Another question remains: why should the cell persist?
The red blood cells have protective systems to help them persist despite the lack of a genetic toolset. One obvious example is the cell membrane, which stays fairly intact for around 120 days. A more subtle one is the glutathione system.
This glutathione system is responsible for clearing oxygen radicals that build up inside the cell. Usually, cells make energy by the membrane enzyme inside mitochondria, ATPase. When this membranous system is affected, the chaotic electrons can create free radicals. These can wreak havoc inside cells.
Several systems inside a cell are present to prevent such occurrences from happening. If it becomes too difficult to control these radicals, the cell commits suicide. This is the mitochondrial pathway towards the common physiological process of apoptosis.
Red blood cells don’t have such membrane-bound organelles to execute these steps. The mop out the radicals using the glutathione. Lose one tool and get another. The cell continues to persist.
Persistence of the whole, in the absence of a part, is what Organismal Selection is all about. More on that later.
Red blood cells eliminate the house of the complete genome because they can. If the gene-centered view is to hold weight under this scrutiny, it does not have any window of explanation once the gene is eliminated. Natural selection can, but not the gene-centred view.
Genes as tools
We personify genes to make sense of them. To call them tools may seem harsh.
But consider employees inside a company. They are tools used by the company. They work efficiently, reporting to work on every weekday. If they fail to comply or are considered redundant, they are eliminated.
Genes are hardly any different.
You can personify or think of them as tools; whatever rows your boat.
A historical tracing of the mitochondrial genes finds their home in alpha-proteobacteria. These bacteria have retained most of their genes because they have no shelter like ours. They have no one to grant their genetic tools.
But once upon a time, one of them joined forces with another prokaryote joined forces. Since they could make energy through their membranes and still replicate, housed by the host, it had a fairly stable environment. Plus, more genes mean more energy. So it extruded most of them.
As it did, it told the host:
Here are my bacterial tools. Use them wisely.
And the host, like Anakin Skywalker, conceded.
However, mitochondria, unlike red blood cells, did not let go of all their genes. They preserved the ones essential to energy production. A pact of sorts was made, allowing each side of the agreement to survive. An organelle related to the mitochondria, hydrogenosomes, has eliminated the whole genome, like the red blood cell. They, however, preserved their ability to produce hydrogen, which was used by the host to make energy.
The host would create a peaceful environment for the once-alphaproteobacteria. The bacteria would produce energy. At the same time, the host needed to bleed the bacteria of extra molecules of energy to prevent the formation of radicals (the level of detail for this extra bit is unnecessary at this point).
What hydrogenosomes, mitochondria, and red blood cells agree on is that genes can be retained or extruded as needed. The gene-centred view of evolution cannot say much about these changes. Another theory of evolution can.
Organismal Selection
Organismal Selection is a novel theory that banks on the universal need for mergers between and among organisms.
In the same way, we can either personify or objectify genes, organisms can take whatever interpretation and create the underlying principle — the need for stable mergers for persistence. In this case, the mitochondria, hydrogenosome, or red blood cell can be viewed as an organism as much as the host.
A merger is stable if the role of one entity improves the persistence of another and vice versa. The role of the host shelter these organelles. The role of the organelles provide energy for the host.
The role of the host increasing in size creates more room for more organelles. The organelles can continue to produce more energy at a cost-effective rate.
The coherence of functions underpins the sustenance of stable mergers. I have mentioned how the host needs to bleed the mitochondria of the excess energy molecules. The reason is, once all the nascent molecules (ADP) are converted into energy molecules (ATP), electrons, which are essential to their generation, lack functionality. They quickly run into oxygen and generate free radicals that can cause injury to cells.
We don’t want that.
So the host developed a nanomachine to remove excess ATP from the endosymbiont. This helps the endosymbiont from dying. They return the favour by continuing to produce energy. That is a sustainable and stable merger.
It’s also a statement about the coherence of functions. No need to reduce the window to a gene-centered view. It also explains other cellular mechanisms, such as the glutathione system, which is not dependent on genes after they have been released through enucleation and mitophagy.
It also explains the persistence of these cells even after the elimination of the full or partial genome — for mitochondria, hydrogenosomes, and red blood cells.
What I’m trying to say is…
We have evolved to the point of generating intelligent machines on the verge of changing our civilization.
We owe it all to the tools handed over to us by the microscopic entities.
Persistence persists past the genes and genomes. And if mitochondria are to have a say on our rise to world dominance, they can utter the lines of Jay-Z:
I’m supposed to be number one on everybody list
We’ll see what happens when I no longer exist
We wouldn’t be here without them.
This song inspired some of the lines used in this article. Source — YouTube