The genetics of extraterrestrial life

Recently someone shared a link about scientists at Sheffield University discovering extraterrestrial life. The scientist captured diatom frustules at 25 km above ground and they argued that it was impossible for it to have come from Earth and that it made more sense that it comes from the watery environment of a comet. In a different report it was suggested that certain structures in meteorites resembled cyanobacterial microfossils and that it was impossible that this was contamination from planet Earth.

 

I believe it is pretty much certain that life originated more than once in this Universe and I would dare to say that we will find life in other places from the Solar System, such as Mars, Europa, Enceladus and even Titan. However, if we discover life in other planets there are a few predictions or assumptions that we can make about their genetics that could give us a better understanding of the origin of life on Earth and the Universe. These predictions are based in what we know about the evolution and diversification of life on Earth.

Case one – Life originated somewhere else in the universe and seeded planet Earth with life.

One of the things that we know about life on Earth is that every single organism in this planet so far discovered, be it a bacterium, an ant, a fungi, or people, is descendant from a common ancestor, which originated (or came to Earth) around 3.8-4.0 billion years ago.

We know this because we share the same genetic system, same molecules of DNA, RNA, proteins… we share many genes and proteins that fulfill similar roles, the back bone of our metabolism is pretty much the same for all life on Earth. This means that IF life arrived to Earth from somewhere else, it did so only once 3.8 to 4.0 billion years ago and only one linage, a unicellular organism, gave rise to all the diversity we know now.

Every single organism we know, cyanobacteria and diatoms, all plants, all sorts of bacteria, all mammals and insects, all fishes and birds, all originated and evolved in planet Earth and nowhere else.

Let’s take the case of diatoms, diatoms are phytoplankton, they are marine algae. We know from fossils and genetics that diatoms originated around the Jurassic time, that is approximately 185 million years ago… possibly they have an earlier origin no further than 250 million years ago. This means that they evolved only recently in geological time. Diatoms are eukaryotes; since they are algae they do photosynthesis. The chloroplast of diatoms originated from a process called secondary endosymbiosis where the ancestral eukaryote diatom stroke a partnership with a red algae… red algae are also eukaryotes that do photosynthesis and also had a chloroplast, which originated in a process called primary endosymbiosis in which the ancestral red algae stroke a relationship with a cyanobacteria. Red algae and plants have one common ancestor. Thus we can trace the full history of diatoms based on the genetics of its genome, its chloroplasts, and the fossil record to events that are only possible to have occurred on planet Earth, and in consequence we can be pretty sure that they originated on planet Earth and nowhere else.

Diatom frustules

If the diatoms in the study at Sheffield University came from outer space they might have been kicked out from planet Earth by some mechanism in the last 250 million years and then returned. Maybe the meteorite that killed the dinosaurs sent some debris to space and stayed orbiting around the planet or the inner solar system. The same thing can be said of cyanobacteria fossils in meteorites, cyanobacteria are earthlings we are absolutely sure due to genetic studies and the fossil record that they originated and diversified on Earth.

Case two – Life as we know originated on Earth but we discover life somewhere else that had a different origin.

Let’s say that we send a mission to Jupiter’s moon Europa and in the inner oceans we find life. Let’s assume that life in this moon originated separately from life on Earth, thus it is a second origin of life independently from Earth’s origin. Or say for example we discover a comet that originated from another part of the galaxy where life evolved as well, independently from life in this planet, a completely different origin. What can we expect then from this life form?

IF life in these samples has a different origin it must then have a completely different genetic system to the one we find on Earth. The first expectation should be that it might not have DNA or RNA as genetic information molecules, but other completely different type of nucleotides or chemical compounds. Say that by coincidence the ingredients for life in this foreign moon or planet were similar to the ingredients of life on Earth so they also have DNA or RNA as their molecules to carry information. Then we should expect that the genetic code and the amino acids that they encode are of a completely different sort to the ones on Earth. There are hundreds of different amino acids; however Life on Earth use 20 very specific ones encoded in a very conserved genetic code. The chances that life which originated independently in another region of the universe uses the same genetic code to encode the very same 20 amino acids that life uses on Earth is rather small. 

But then less assume that just by chance, this independent origin of life used the same nucleotides and amino acids as it did on Earth… since it originated and evolved somewhere else at the very least every single gene, given the chance that this life also has “genes”… their sequences have to be radically different to the ones on Earth. The metabolism and physiology of these extraterrestrial organisms must be of a completely different type, optimized and specialized for the environments found in the moon or planet where it evolved. Just minute differences in the light intensity of the sun, the rotation of that planet (or moon), the weather, the different concentration of gases in the atmosphere or the salts of its oceans will lead to completely different sorts of genetics and biology to that on Earth, and more necessarily so if it originated separately and independently from Earth.

Thus even if the probability that life originated independently in a different planet is high, the chances that it evolved to exactly the same organisms as in planet Earth, the chances that a cyanobacteria or a diatom sprung from that separate origin, sharing thousands of the same genes, encoding for exactly the same proteins that exist on planet Earth are pretty much none. Unless they come from a parallel Earth in a parallel Universe.

Case three – Life on Earth originated somewhere else and seeded not only Earth but many other planets and places in the universe, and then now we find a comet with a life from another planet but sharing the same origin of life with us.

As I mentioned before ALL life on Earth that we know of descends from a common ancestor 4.0-3.8 billion years ago. This does not change, this is a fact.

Let’s then assume that life originated before, for example 6.0 billion years ago and somehow it spread throughout the universe… one linage from this origin seeded Earth 4.0-3.8 billion years ago. This implies that life on Earth have been evolving independently for billions of years.

Say now that the extraterrestrial life we found, before arriving to Earth, landed billions of years ago in another planet or moon, it thrived there evolving into many different forms and diversifying, then something happened and a sample of life from that planet reached Earth today. Thus, we should expect that since this extraterrestrial organism shared a common ancestor with terrestrial life at least 4.0 billion years ago it shares the same genetic system that life on Earth: DNA, RNA, proteins composed of the same amino acids, even similar cellular structures. HOWEVER, because Earthlings and extraterrestrials evolutionary paths separated before life diversified on Earth, this implies that every form of life on earth is more similar to each other, or shares a more recent common ancestor, that this Earthling ancestor is to the extraterrestrial organism. When comparing their DNA or proteins in an evolutionary tree, we must see that all life on Earth should make one branch and the extraterrestrial a separate one as in the tree I show below. This should be evident from their genetic sequence. Since the earthling and the extraterrestrial share a common ancestor they might share many traits, yet because the extraterrestrial organism has been thriving in another planet it should have also many unique characteristics that evolved to adapt itself to the environment it lived.

Phylogenetic tree of a hypothetical extraterrestrial organism sharing a common ancestor with all Earthlings

There is another possibility: the sample of life we find in the meteorite or in space might be the same as the common ancestor of all earthlings, but it had been frozen in space for billions of years and now we find it. Because all life on Earth shares many characteristics, we know what traits the common ancestor must have had. Thus we should find these characteristics in the extraterrestrial sample. This should also be evident from the sequence information of its genome.

In conclusion, if we find life out there we will know for sure once we examine their genetics and their characteristics. Also if we find cyanobacteria or diatoms in space they must have originated in planet Earth one way or another, no doubts about it.

Quinone binding in Type I reaction centers from Heliobacteria

I have been recently reading about the interesting photosynthetic reaction center found in Heliobacteria. I think one of the most striking things about it is the debate and discussions about whether the Heliobacterial reaction center (RC) binds a quinone or not. The most recent and better purification strategy showed that there was 1.6 menaquinones per RC. They suggest that this could be interpreted as 64% of the centers having both quinones bound, 32% with one quinone bound and one empty site, and 4% with no quinones at all. Whatever the case the most likely interpretation about the whole debate―that has been going on for several decades as a matter of fact, is that the menaquinones in the Type I RC from Heliobacteria are loosely bound...  the question is why and what is the relevance of this feature.

I wanted to see how the phylloquinones in Photosystem I are bound to the protein. You can see the figure below that most of the quinone is pretty much in a hollow space.

The head of the quinone interacts with the protein by a single hydrogen bond and by hydrophobic interactions to a tryptophan and phenylalanine side chain, see below.

Not only that, but the tail is surrounded by five chlorophylls and a carotenoid molecule, approaching within 4 Å of the quinone, see below.

To top it all, these are held together by some of the smaller peripheral subunits:

So, no wonder why the quinones of PSI are so well bounnd.

In the case of the Heliobacterial reaction center, the tryptophan and phenylalanine are not conserved; there is only one carotenoid molecule (4,4'-diaponeurosporene) in comparison to 22 β-carotenes in Photosystem I; there are only about 20 chlorophylls in compared to about 96 in Photosystem I from Thermosynechoccocus; and there are no peripheral subunits. So, if the folding of the Heliobacterial reaction center protein is similar to Photosystem I, then the quinones will be very exposed.

I think a really interesting possibility is whether the Heliobacterial Type I could have a quinone reduction activity like in Type II reaction centers under certain conditions: this is the more likely when you consider that the PshB protein that should hold the terminal electron acceptors F(A) and F(B) is also loosely bound.

Ethanol production using heterocyst-forming cyanobacteria

Cyanobacteria are of great biotechnological interest for their potential to produce biofuels driven by oxygenic photosynthesis. In other words, you can make biofuels from sunlight, water, and CO₂. One approach is to produce ethanol: in order to do this a couple of enzymes need to be introduced using genetic engineering to metabolize pyruvate to ethanol. Arguably, the most successful of this is that by company Algenol were they introduced pyruvate decarboxylase and alcohol dehydrogenase from the alpha-proteobacterium Zymomonas mobilis into the marine unicellular cyanobacterium Synechococcus sp. PCC 7642. This approach was patented and in the patent it is said that rates of 1.7 µmoles of ethanol / mg chlorophyll-a / hour were obtained, which in my opinion is a very modest rate. Certainly, it is below 1% of the rates of Photosystem II activity under saturating light. Algenol is now producing 10000 gallons / acre / year, what appears to be a promising yield... and if the life cycle analysis they published is correct, the energy balance is positive: in other words, there is more energy in the ethanol produced than it was invested to drive the company and purify the ethanol.

Here I want to propose an alternative approach that I think will generate better yields. This is based on quantitative proteomic results in multicellular cyanobacteria capable of differentiating heterocysts. Under nitrogen starvation multicellular filamentous cyanobacteria differentiate 5-10% of their cells into a cell type specialized in atmospheric nitrogen fixation, nitrogen-fixing cells are called heterocysts. Heterocysts contain nitrogenase and other oxygen intolerant enzymes and for that reason photosynthetic oxygen evolution is inactivated or slowed down in the heterocysts. However, the surrounding cells are still capable of oxygenic photosynthesis and they transfer reductant to the heterocysts in exchange for fixed nitrogen in the form of glutamine.

A, Filamentous cyanobacteria, the arrow points to a heterocysts. B, Isolated heterocyts.

The proteomic work by Ow et al. (2009) indicated that heterocysts from Nostoc punctifurme contained very large amounts of the enzyme pyruvate kinase which uses phosphoenolpyruvate to generate ATP and pyruvate. In this study it was shown that pyruvate kinase was at least 3.8 times more abundant in the heterocysts compared to the vegetative cells. This predicts that heterocysts might have naturally higher concentrations of pyruvate. The reason why pyruvate is in higher concentrations in heterocysts is because it is the precursor of 2-oxoglutarate, which is the precursor of glutamate. In heterocysts glutamate reacts with ammonia (the product of atmospheric nitrogen reduction by nitrogenase) to produce glutamine.

My idea is to express pyruvate decarboxylase and alcohol dehydrogenase from Zymomonas or Saccharomyces in the heterocysts of a multicellular cyanobacterium, such as the fresh water Nostoc sp. PCC 7120, Nostoc punctiforme or Anabaena variabilis or a marine version like Anabaena sp. 90. The technology to do this is already in existence. Since the metabolism of heterocysts is super-ramped up to provide nitrogen for 90-95% of the cells, I am pretty sure that the yields of ethanol could be pretty high.

It does not come without challenges because probably the diversion of pyruvate to generate ethanol might impair to certain extent nitrogen-fixation, however it has been shown that heterocysts can compensate a loss of reducing equivalents by boosting up cyclic photosynthesis and probably their own metabolism. It might be that a lack of pyruvate could enhance carbon-fixation, a bonus. In any case, we will not know if this is a sound idea until we try it out.

Trichoplax adhaerens, a weird animal with a piece of Photosystem I

I was doing a BLAST of the PsaA subunit of Photosystem I (PSI) restricted to Metazoans and found that the organism Trichoplax adhaerens had a fragment of 141 amino acids of this subunit. The predicted amino acid sequence from T. adhaerens has 97% similarity to that of the diatom Synedra acus.

T. adherens is a  placozoan, a basal eumetazoan, in other words a very ancient animal.

It encompasses the region of PsaA from amino acid 615 to 755 using the numeration of the crystal structure from Thermosynechococcys elongatus 1jb0. This region contains the last two transmembrane helices of the PsaA subunit where some of the redox active chlorophylls are coordinated (see figure 1).

Figure 1. Cartoon model of the PsaA subunit from T. elongatus. In sand color the section of protein that is encoded in the PsaA fragment from T. adherens.

Because of the high similarity of the sequence to that of the diatom, and due to the fact that animals do not have photosystems, we can safely assume that it is an event of horizontal gene transfer... possibly too, contamination.

I will check if there are more fragments of photosynthetic proteins in this animal and report here if I find something else.