Conserved lipids in photochemical reaction centers

Back in 2001, Wakeham et al. (2001) wondered whether a lipid molecule found in the Type II reaction center from Rhodobacter sphaeroides (Fig. 1) was conserved in all anoxygenic Type II reaction centers.

Fig. 1. Cardiolipin binding in the Type II RC from Rhodobacter sphaeroides, 1qov. The M subunit is shown in orange and the L subunit in gray. Cardiolipin is displayed as spheres.

Similar lipid binding sites in Photosystem II (Fig. 2 and 3) and in Photosystem I (Fig. 4 and 5) can be seen in the crystal structures. However, unlike the reaction center from R. sphaeroides, which appears to bind only one cardiolipin, Photosystem II and Photosystem I bind lipids symmetrically on both sides of the reaction center. In the crystal structure from plant Photosystem I only one 1,2-distearoyl-monogalactosyl-diglyceride (3lw5) was found in a similar position to the one in Synechococcys elongatus. I suspect the symmetrical counterpart was not seen because of the low resolution.

Fig. 2. 1,2-dipalmitoyl-phosphatidyl-glycerol and sulfoquinovosyldiacylglycerol binding in Photosystem II from Thermosynechococcus vulcanus, 3wu2. The D1 subunit is shown in orange and D2 in gray. The lipids are displayed as spheres.

Fig. 3. Symmetrical binding of lipids in Photosystem II.

Fig. 4. Binding of 1,2-distearoyl-monogalactosyl-diglyceride in Photosystem I from Synechococcus elongatus, 1jb0. The PsaB subunit is shown in orange and the PsaA in gray. The lipid is shown as spheres.  The antenna domain has been omitted for clarity.

Fig. 5. Like in Photosystem II, the lipids bind symmetrically in Photosystem I.

It appears then that the binding of lipids in that position is a conserved feature of all reaction centers and might have existed in the primordial reaction center at the dawn of photosynthesis. It is possible that in each type of reaction center the role of these lipids have changed. I found a paper that suggested that cardiolipin affects charge recombination in R. sphaeroides (Giustini et al. 2005).  But in Photosystem II the role of this lipids might be more related to assembly and repair, besides specific structural roles (Mizusawa and Wada 2012). The role of these lipids found in Photosystem I is less clear but it has been suggested that they might influence the phylloquinones in some manner (Fromme et al. 2001).

References
Fromme, P., Jordan, P. & Krauss, N. Structure of Photosystem I. BBA-Bioenergetics 1507, 5-31 (2001).

Giustini, M. et al. Influence of cardiolipin on the functionality of the QA site of the photosynthetic bacterial reaction center. J Phys Chem B 109, 21187-21196 (2005).

 Mizusawa, N. & Wada, H. The role of lipids in photosystem II. BBA-Bioenergetics 1817, 194-208 (2012).

Wakeham, M. C., Sessions, R. B., Jones, M. R. & Fyfe, P. K. Is there a conserved interaction between cardiolipin and the type II bacterial reaction center? Biophys J 80, 1395-1405 (2001).

Photosynthetic constraints on fuel from microbes

The question is, are biofuels really a solution to the global energy crisis? Are they really sustainable? The main issue is the low photosynthetic efficiency of solar energy conversion to fuel or biomass. The efficiency is so low that the amount of energy obtained in the biofuel is apparently lower than the energy that was invested to produce it.

Perhaps it is possible to enhance photosynthesis to the point that biofuels become truly a solution... in our recent opinion paper we have discussed some recent approaches at improving photosynthesis.

Photosynthetic constraints on fuel from microbes

Grown algae - By IGV Biotech (Own work) [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons

The origin of oxygenic photosynthesis in Cyanobacteria (some thoughts)

The last common ancestor to all extant cyanobacteria had already evolved the capability to oxidize water as the earliest known diverging species of cyanobacteria of the genus Gloeobacter have a fully evolved Photosystem II. For example, Gloeobacter violaceous has five D1, D2, the CP43 and CP47, the Cyt b559, Cyt c550, PsbO, L, M, J, K, H, T, X, and P [1-3].

It can be deduced with confidence that oxygenic photosynthesis evolved before the last common ancestor of extant cyanobacteria. It suggests a period of evolution that saw the transformation of a simple Type II reaction center incapable of water oxidation into the sophisticated Photosystem II.

The question is: for how long before the last common ancestor of extant cyanobacteria was water oxidation possible? Could water oxidation by a primitive Photosystem II have evolved fast?

The Great Oxygenation Event occurred around 2.3-2.4 Ga ago. I think this time correspond to the major radiation of cyanobacteria… when the major clade of cyanobacteria evolved, but after the evolution of the Gloeobacter genus and early evolving Synechococcus (e.g. Yellowstone strains).

The closest relatives of cyanobacteria that are incapable of oxygenic photosynthesis are the melainabacteria [4, 5]. It appears though, oxygenic photosynthesis appeared some time in between the divergence of the melainabacteria and the last common ancestor of the cyanobacteria. Before this, there is the divergence of the chloroflexi from the lineage that led to cyanobacteria [6]. Because the chloroflexi are phototrophs I dare to suggest that the chloroflexi and the cyanobacteria shared a photosynthetic ancestor that was incapable of water oxidation [7].

Based on molecular clock analysis it’s been estimated that the major phyla of bacteria radiated around 3.2 Ga [8, 9].

Some of the earliest evidence for oxygen on earth date to ~3.0 Ga [10, 11].

So, I speculate that there is about 200 million years for water oxidation to have evolved, starting from the major radiation of bacteria and culminating with the first significant amounts of oxygen detected in the geochemical record.

Evidence of oxygenic photosynthesis before 3.2 Ga… are difficult to reconcile with the overall evolution of bacteria. IF for some unexpected reason strong evidence for oxygenic photosynthesis around 3.8 Ga is found. This should imply panspermia… maybe a rock containing a huge diversity of prokaryotes with all sorts of archaea and bacteria (including fully evolved cyanobacteria) hit earth during the late heavy bombardment. But I don’t think that makes much sense given the available evidence :-)

Sequence of events in the evolution of water oxidation

1. Saw, J.H.W., et al., Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp nov., from a Lava Cave in Kilauea Caldera, Hawai'i. Plos One, 2013. 8(10).

2. Koyama, K., et al., Oxygen evolution in the thylakoid-lacking cyanobacterium Gloeobacter violaceus PCC 7421. Biochim Biophys Acta, 2008. 1777(4): p. 369-78.

3. Kaneko, T., et al., Complete genome structure of the unicellular cyanobacterium Gloeobacter violaceus PCC 7421. Plant and Cell Physiology, 2004. 45: p. S129-S129.

4. Soo, R.M., et al., An Expanded Genomic Representation of the Phylum Cyanobacteria. Genome Biology and Evolution, 2014. 6(5): p. 1031-1045.

5. Di Rienzi, S.C., et al., The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. Elife, 2013. 2.

6. Segata, N., et al., PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nature Communications, 2013. 4.

7. Cardona, T., A fresh look at the evolution and diversification of photochemical reaction centers. Photosynth Res, 2014.Advanced access, 18 of Dec.

8. David, L.A. and E.J. Alm, Rapid evolutionary innovation during an Archaean genetic expansion. Nature, 2011. 469(7328): p. 93-96.

9. Battistuzzi, F.U. and S.B. Hedges, A major clade of prokaryotes with ancient adaptations to life on land. Molecular Biology and Evolution, 2009. 26(2): p. 335-343.

10. Crowe, S.A., et al., Atmospheric oxygenation three billion years ago. Nature, 2013. 501(7468): p. 535-8. 11. Planavsky, N.J., et al., Evidence for oxygenic photosynthesis half a billion years before the Great Oxidation Event. Nature Geosci, 2014. 7(4): p. 283-286.

Reflexions on the origin of photochemical reaction centers

My review paper dealing with the evolution of photosynthesis has been published now in Photosynthesis Research. Please, take a look:

A fresh look at the evolution and diversification of photochemical reaction centers

Phylogenetic tree of prokaryotes

Stages in the evolution of photosynthesis

There are four stages from the origin of life until the appearance of oxygenic photosynthesis.

Stage 1

From no photosynthesis to the origin of chlorophyll and the first reaction center protein.

There had to be a period in time before the origin of chlorophyll synthesis and photosynthesis. A series of proteins evolved to turn a porphyrin precursor into chlorophyll and bacteriochlorophyll. Enzymes with homology to nitrogenases were recruited for this purpose. Proteins capable of binding chlorophyll or its precursors had to evolve before photosynthesis. This include a membrane protein that would evolve into a reaction center capable of light-driven charge separation.    

Stage 2

The first homodimeric reaction center diverges into two classes presumably both homodimeric: a Type I and Type II reaction centers.

Stage 3

The primordial Type II reaction center protein diverges into two distinct classes. One class of protein is the ancestral to the PufL and PufM proteins in photosynthetic Proteobacteria and Chloroflexi. The other class is the ancestral to D1 and D2 proteins in a lineage that would be the progenitors of Cyanobacteria. 

Photosystem I (PDB ID: 1jb0)

Stage 4

Starting with a homodimeric Type II reaction center, in the lineage that would be a progenitor of the Cyanobacteria, a gene duplication occurs that drives the divergence of D1 from D2. At some moment that could have started even before D1 and D2 diverged, the capacity to oxidize water appeared. The homodimeric Type II reaction center then becomes heterodimeric and gains incredible complexity to evolve into the Photosystem II characteristic of Cyanobacteria.

The last common cyanobacterial ancestor had already a fully developed oxygenic photosynthetic machinery implying and unknown biota of cyanobacteria, this is because the earliest branching cyanobacteria from the genus Gloeobacter, already possesses a fully developed Photosystem II and Photosystem I. This implies an unknown biota preceding the last common cyanobacterial ancestor.

Photosystem II (PDB ID: 3arc)

The key question is, how long it took from the origin of photosynthesis to the appearance of water oxidation. If we assume that the first water splitters originated around 2.7 to 3.0 billion years ago, and the origin of photosynthesis between 3.8 to 3.3 billion years ago, the completion of these four stages could have taken anything from 300 million to 1.1 billion years.

Knowing the speed at which bacteria evolves and the lengths of time we are talking about, hundreds of millions of years, each one of these stages should have given rise to a significant diversity. Most of which appears to have gone extinct.

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.