Solar powered: the evolution of photosynthesis

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Kat: Most of the time, when we talk about DNA or genomes on this podcast, we’re talking about eukaryotes – that’s pretty much everything on the evolutionary tree from yeast upwards, so that’s fungi, animals and plants, plus single-celled organisms called protists. The word eukaryote means ‘true kernel’ (or perhaps ‘well nutty’, depending on your attitude to Greek translation), referring to the fact that these are organisms whose DNA is packaged up within the confines of a structure called the nucleus – a kind of biological bag that can be clearly seen down a microscope as a round, or kernel-like shape inside each cell.

There are several ways to think of the nucleus: as a central library, storing the instructions encoded within DNA safely so they can’t be damaged by the hurly-burly of biological processes in the rest of the cell. Or maybe we can envisage it as a control centre, directing the activity within the cell and switching genes on or off in response to cues from a changing environment. Either way, the nucleus is the place where the action is, when it comes to genes and genomes.

But there’s far more to life on earth than eukaryotes. There’s also the world of prokaryotes – single-celled bacteria and closely-related archaea, which lack a nucleus and leave their DNA to roam free – as well as viruses, which are little more than a strand of genetic information, either DNA or RNA, packed inside a protein coat.

Sally: Are viruses really alive though?

Kat: Shush, Sally – not now. Take it to Twitter…

Anyway. This time, I wanted to take a closer look at where the lines between these worlds starts to blur. It’s time to go back – way back, to where it all began.

Solar powered: the evolution of photosynthesis

“In the beginning God created the heaven and the earth. And the earth was without form, and void; and darkness was upon the face of the deep. And the Spirit of God moved upon the face of the waters. And God said, Let there be light: and there was light.”

Now, I’m not for a minute suggesting we take the King James Bible as a scientific explanation for the origins of life. But these beautifully poetic words from the book of Genesis highlight the fact that the light from the Sun has been the biggest source of energy for the Earth since the formation of the planet 4.5 billion years ago.

It would take a further 1 billion years or so for life to emerge in the form of simple bacteria-like cells – something we explored back in episode 17 of series 4, Back to the Beginning – but pretty soon after that, these early organisms figured out how to do something that would literally change the world. And that thing? Photosynthesis.

If you cast your mind back to your school biology lessons, you’ll remember that photosynthesis is the process by which plants harness the energy in sunlight to produce food and oxygen from nothing more than carbon dioxide and water. Easy, right?

Although it sounds simple, the underlying processes of photosynthesis are incredibly complex – detailed circuit diagrams that I had to memorise for my degree, involving multiple different enzymes and chemicals and electrons being shuffled about all over the place. But, of course, these processes didn’t just appear out of nowhere – they had to evolve, becoming encoded within genes and passing down countless generations from the very earliest photosynthetic bacteria to the rich diversity of green stuff on the planet today.

However, while we usually associate photosynthesis with taking in carbon dioxide and water and producing oxygen, the very first photosynthesisers on Earth probably didn’t actually produce oxygen at all.

The exact nature of the first photosynthetic organisms and precisely when they appeared are still subjects of some controversy. There’s evidence of what look like photosynthetic bacteria in the early fossil record, in the form of finely stranded textures in rocks dated around 3.5 billion years ago. 

At this time there was plenty of carbon dioxide and water in the atmosphere around the early Earth; the inputs needed for photosynthesis. But, oddly enough, we don’t see significant evidence of there being much oxygen around in the atmosphere until nearly a billion years later. So what was going on?

To find out, let’s take a step back to look at what the underlying chemical reaction of photosynthesis actually is.

The word itself means ‘to put together using light’. The things that are being put together are molecules of carbon dioxide, creating carbohydrate molecules such as sugars and other molecules that form the building blocks of living cells. To do this requires energy in the form of electrons, which are produced by using light to split them off from a molecule known (obviously enough) as an electron donor.

In case you’re wondering how this works, the light is captured by chlorophyll – a colourful, complex chemical containing the metal magnesium trapped in a ring of nitrogen, carbon and oxygen, which absorbs light and uses that energy to shuffle electrons and hydrogen ions around from one place to another – a bit like a tiny solar cell converting sunlight into electricity.

In most photosynthetic organisms the electron donor is water – a molecule made of two hydrogen atoms and one oxygen atom, hence H2O, which is split up into its constituent parts and releases oxygen back out into the atmosphere – that’s called oxygenic photosynthesis. But it’s also possible to use hydrogen sulphide, H2S, as the electron donor instead.

Better known as the eggy-smelling component of farts, hydrogen sulphide was abundant on the early earth, released by volcanic eruptions and providing plenty of electron donors for the first photosynthetic bugs. Photosynthesis using hydrogen sulphide instead of water would produce sulphur instead of oxygen. 

So, given the lack of oxygen appearing in the environment, and the fact that the enzymes involved in sulphur photosynthesis appear to be simpler than those for water and oxygen, it’s generally accepted that the first photosynthetic organisms on earth used this sulphur-based anoxygenic version of photosynthesis – although this view is being challenged as new evidence and thinking comes to light.

The Great Oxygen Catastrophe

Whatever really happened back then, the current narrative holds that the switch to using water for photosynthesis, together with the production of oxygen, came with the evolution of cyanobacteria, around 700 million years after the initial sulphurous species. Also known mistakenly as blue-green algae, these photosynthetic bugs thrive in a wide range of environments, and were the first organisms on earth capable of producing oxygen. And with them came what became to be known as the Oxygen Catastrophe, or the Great Oxidation Event, if you’re less of a drama queen.

Take a nice deep breath. Enjoy the heady blend of 78 percent nitrogen, 21 percent oxygen and just 0.04% carbon dioxide filling your lungs. But it wasn’t always like this.

If you could invent a time machine and take a trip back 3 billion years, you wouldn’t last long. A lungful of air would leave you suffocating on a toxic mix of mostly carbon dioxide, with a bit of nitrogen, methane, ammonia and water vapour thrown in for good measure, and virtually zero free oxygen. But once oxygen-producing photosynthetic bacteria appeared on the scene, that all changed. Slowly but surely, these little bugs began to destroy the world.

Initially, oxygen levels on the early earth began to rise gradually, as the gas was absorbed first within the oceans and then by the land. But eventually it was all too much. By 2 billion years ago, photosynthetic bacteria had pumped out enough oxygen to fill a staggering 35% of the earth’s atmosphere in a relatively short space of time, before dropping down closer to what we breathe today.

You probably associate oxygen with health, life and vitality, but it’s highly toxic to organisms that haven’t evolved to deal with it. The rapid rise in oxygen levels was catastrophic for the majority of bacterial species on Earth at the time, which had evolved in an oxygen-free, anaerobic environment, creating what could be described as a mass extinction event. But as anaerobic bacteria bit the dust, a new wave of organisms emerged, including the very first eukaryotic organisms, paving the way for the evolution of fungi, plants, animals and, eventually, humans.

After cyanobacteria came the sea plants: red and brown algae, which turned up around 1.2 billion years ago, followed by green algae half a billion years later. The first simple land plants – ground-hugging mosses and liverworts – evolved less than 500 million years ago, while plants with stems came a bit later. And here we are – breathing oxygen produced by plants, eating them, feeding them to other things so we can eat them instead, wearing clothes made from them, living in structures built from them, writing on paper produced from them, and on and on and on –all powered by sunlight, and thanks to some humble blue bacteria that wrecked the planet a couple of billion years ago. Life, as ever, finds a way.

Image by Kelvinsong via Wikimedia Commons

On the origin of chloroplasts

It might seem that today’s photosynthesising plants are a long way from the cyanobacteria of three billion years ago, but actually they’re a lot closer than you think.

In episode 23 of our very first series back in 2019, Mergers and Acquisitions, we told the story of Lynn Margulis – a visionary biologist who pioneered the idea that reason why the structures within plant cells that carry out photosynthesis, known as chloroplasts, might look a bit like bacteria – even down to having their own DNA that looks a lot like bacterial DNA - was because they were originally just that: photosynthetic bacteria that had set up home within larger plant cells at some point way back in time, triggering a major leap forward in evolution.

Every superhero needs a good origin story, and chloroplasts are no exception.

It’s the year minus 2 billion… or maybe minus 1 billion. Or somewhere between the two. Who knows? We zoom in on a field of primordial cells feeding on cyanobacteria, scooping them up with a fold of cell membrane to create a little pocket inside themselves, known as a vacuole, so they can digest the bugs at their leisure. 

One of them – our intrepid hero – manages to break free before it becomes dinner, escaping into the interior of the cell and starting to proliferate. But rather than being ejected or eliminated, this lucky bug and its descendants prove their worth to the host, using nothing more than light, water and carbon dioxide to churn out a constant source of food. Ok then, I guess you can stay.

Fast-forward a few million years, and chloroplasts are fundamental to generating food and oxygen to sustain life on this planet, and the relationship between these plucky bugs and their plant hosts is unbreakable. And I do, literally, mean unbreakable. Although the original bacterium came with a full set of DNA containing all the genes and molecular machinery it needed to survive as an independent entity, over time many of these genes got lost or became assimilated within the genome of the host cell. Today’s chloroplasts have just 130 or so genes, compared with a likely starting number of around 3,000 back in the day, with many tasks outsourced to the machinery of the cell rather than done by the chloroplast itself.

Despite its small size, the chloroplast genome has attracted a huge amount of attention in recent years as a target for genetic modification. Plant genomes are huge and complex, often the result of multiple genomes mashed together or duplicated. Even with the latest genome engineering tools it’s hard to accurately modify a plant gene and get it to do what you want. 

Because the chloroplast DNA is much more similar to that found in bacteria, with far fewer genes and simpler regulation, it’s a lot easier to get in there and fiddle around. And because chloroplasts are maternally inherited – they come prepackaged in the egg cells produced by female plants rather than wafting about all over the place in male pollen grains – there’s less risk that modified genes can escape and spread into other species.

Perhaps the most obvious use of chloroplast genetic engineering is in the development of plants that are more efficient, naturally pest-proof, or resistant to environmental stresses such as hight salt and drought. But there are other ideas too, such as creating GM plants that can mop up toxic metals like mercury from the environment, produce vaccines, drugs, enzymes or other valuable products in the leaves, fruits or roots, or even generate environmentally sustainable biofuels. And advances in synthetic biology are making chloroplast engineering ever more easy and efficient – so it’s definitely, if you’ll excuse the pun, a growing field (I’m so sorry).

Ever decreasing circles

Finally, I want to leave the world of chloroplasts and their genomes by flagging a curious controversy that I uncovered while researching this story. Now plants – like animals – keep their DNA in the form of chromosomes that are linear strands of DNA, like a shoelace with two ends. But bacterial chromosomes are circular. Now, given that I’ve just told you that chloroplasts originated from bacteria, you’d expect their chromosomes to be circular too. And, according to pretty much everyone, they are. Or are they?

As far back as 1962, scientists discovered that chloroplasts contain their own DNA. By the mid-70s researchers were using early molecular biology tools to start mapping out the genes within them, and by 1980 the first gene had been sequenced. Given the small size of the entire chloroplast genome, it wasn’t long before the genomes of tobacco and liverwort had been read, and by the end of 1996 nine chloroplast genomes from different plant species had been fully sequenced. As of 2020, chloroplast genomes from more than 3,700 plant species have been sequenced, revealing important information about their function and symbiotic relationship with plant cells.

For a long time, the techniques used to read and put together DNA sequences have all pointed towards chloroplast DNA being circular, just like their bacterial progenitors. But one researcher – Arnold Bendich from the University of Washington in Seattle - has long argued that this might not actually be the case.

In a 2004 paper in the journal Plant Cell he says,

“If we could extract, purify, and visualise the intact DNA molecules from chloroplasts, what would those molecules look like? Most would expect to find circular DNA molecules the size of the chloroplast genome. By contrast, however, only a small fraction of the DNA obtained from chloroplasts is found as genome-sized circles. I will trace the history of research on chloroplast DNA to elucidate why it has taken more than 30 years to realise that the circle is not the principal form of DNA in chloroplasts and to examine the relationship between the chloroplast genome and the segregating genetic unit or chromosome in chloroplasts. The critical finding is that the chloroplast chromosome can contain many genome equivalents.”

Bendich points out that we think that chloroplasts have circular chromosomes because all the DNA mapping sequencing techniques that were used to analyse them are designed to spit out results as circular chromosomes, so anything that doesn’t fit this pattern must be the result of broken circular chromosomes, and not any kind of naturally-occurring chromosomal structure – a neat bit of circular reasoning. 

Detailed analysis of a number of plant chloroplasts in species such as maize and alfalfa has shown peculiar linear and branched DNA structures, particularly at times when there’s a lot of DNA replication going on, suggesting that chromosomes are more complex than simple circles, at least some of the time, and for at least some species.

In another paper from 2015, Bendich and his colleague Delene Oldenburg argue,

“The bacterial origin of [chloroplast] DNA appears to have profoundly influenced ideas about the properties of chromosomal DNA molecules in these organelles to the point of dismissing data inconsistent with ideas from the 1970s. When found at all, circular genome-sized molecules comprise a few percent of [chloroplast] DNA. In cells active in [chloroplast] DNA replication, most [chloroplast] DNA is found as linear and branched-linear forms larger than the size of the genome, likely a consequence of a virus-like DNA replication mechanism.”

Bendich concludes his 2004 paper by stating, “There are lessons to be learned about how to interpret data that initially seem at odds with popular thinking. Chief among them is that complex DNA structures should not be dismissed simply because they do not meet our expectations for a chromosomal DNA molecule: simple in form and genomic in size.”

But while he makes an impassioned argument that chloroplast chromosomes might not be the simple circles that everyone imagines, and that the field has fallen prey to groupthink, I’m always wary when it’s just one lab, or even just one scientist, banging the drum for a particular scientific idea, even though the history of science tells us that at least some of the time they turn out to be right. 

However, looking away from chloroplasts and to another organelle inside plant cells – mitochondria, which are the cell’s power stations – the latest research shows that while simple circular maps may be a handy way of drawing mitochondrial genomes, the reality is much more complex, with all manner of structural shenanigans including linear and branching chromosomes.

A 2019 paper from plant scientists at University of California Davis highlighted this alternative chromosomal reality, saying,

“Plant mitochondrial genomes are commonly depicted in research articles and textbooks as circular molecules that are the size of the genome. Although research on mitochondrial DNA over the past few decades has revealed that genome-sized circles are exceedingly rare and that alternative forms of mitochondrial DNA are more common, many biologists still perceive circular maps as representing one or more physical chromosomes. This misconception can lead to biases in how mitochondrial genomes are assembled and misinterpretation of their evolutionary relationships, synteny, and histories.”  

So, what’s the message here? That chloroplast chromosomes may be straight, not circular, especially when they’re actively replicating? That we need better tools for studying DNA in dynamic situations in living cells and organelles? Little of column A, little of column B? If you’re a plant geneticist I’d love to hear from you about what you think, and whether you’re Team Linear or Team Circular. You can tweet us @GeneticsUnzip, or email podcast@geneticsunzipped.com to share your thoughts.