March 30, 2023

A tiny creature illuminates an important biological advance

A tiny creature illuminates an important biological advance
A tiny creature illuminates an important biological advanceA tiny creature illuminates an important biological advance

THE ROAD to human beings was long and winding. But a big step on it was the first eukaryotic cell. Eukaryotes comprise the living world as it is familiar from TV documentaries: animals (humans included) and also plants, seaweeds, fungi and a host of other types of creature too tiny for the naked eye, but which flit around attractively under a microscope.

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This extraordinary diversity was made possible because, unlike the cells of life’s other two great realms, the bacteria and the archaea, eukaryotic cells have lots of internal structures known as organelles. The division of labour which these organelles permit has allowed eukaryotes not merely to evolve, but to become gradually more sophisticated over the ages in ways that bacteria and archaea have never managed. How organelles came into existence is therefore a matter of great biological interest. And a discovery made recently in the depths of Lake Zug, in Switzerland, has cast a bit more light on the subject.

What lies beneath

Most experts reckon the first eukaryotic cell was a collaboration which happened about 2bn years ago between an archaean and some bacteria. These bacteria were the ancestors of organelles called mitochondria that even today retain their own stripped-down versions of bacterial genomes and which have the specialist task in a cell’s economy of generating energy-rich molecules called ATP that power many cellular chemical reactions.

They usually do this by reacting glucose with oxygen to produce water and carbon dioxide, in a process known as aerobic respiration. But not always. Some eukaryotes live in places with no oxygen, and their mitochondria have evolved accordingly. In a less efficient process known as anaerobic respiration, they churn out hydrogen, rather than CO2. Genetic analysis shows, nevertheless, that these odd mitochondria are still mitochondria. So it came as a surprise to Jon Graf and Jana Milucka of the Max Planck Institute for Marine Microbiology in Bremen, Germany, to discover that the “mitochondria” in some organisms they were looking at, aren’t.

The creatures in question (see picture), which they describe in a paper in Nature, belong to a group of single-celled eukaryotes called ciliates. They live in Lake Zug at such depth that no oxygen comes down to them from the surface. These bottom-waters do, however, make up for that lack by being rich in both methane and nitrates. These are the breakdown products of organic matter swept into the lake and digested by bacteria in the lake bed.

Some other bacteria, called methanotrophs, are able to consume the methane as a food stuff. And some methanotrophs are, in turn, able to use nitrates—which have three oxygen atoms to every one of nitrogen—as an oxygen substitute in a form of respiration known as denitrification that is a halfway house between the aerobic and the anaerobic varieties of that process. This was why, in October 2018, Dr Graf and Dr Milucka travelled to Lake Zug. Their goal was to study its methanotrophic bacteria to see if they, too, were denitrifiers.

To this end, they collected samples from the lake’s depths and sent them to the Max Planck Genome Centre, in Cologne, for analysis. They were searching, in particular, for DNA sequences that looked as though they encoded denitrifying enzymes. And they found some. But not in the way they expected. “We discovered denitrifying genes, but belonging to a genome that was extremely spartan,” says Dr Milucka. “It consisted of only 310 genes, encoding a respiration pathway nearly identical to that of mitochondria—except with a chemistry based on nitrate rather than oxygen.”

That sparsity suggested the genome in question did not belong to a free-living organism. And, with the benefit of further expeditions to the lake, Dr Graf and Dr Milucka now know that it is actually the DNA of a novel bacterium that is well on the way to becoming an organelle, and is hosted by a previously undescribed species of ciliate. Moreover, this bacterium-cum-organelle’s free-living ancestor appears to have taken up residence in the ancestors of its ciliate hosts only 200m years ago. It thus provides a snapshot of the process by which mitochondria themselves formed. It has also proved a success. Nitrate-breathing ciliates related to the one in Lake Zug have spread across the globe. A comparison conducted by Dr Graf and Dr Milucka of DNA samples in a genetic database has revealed closely related species as far afield from Switzerland as the lakes of East Africa’s Great Rift Valley.

Complexity theory

Dr Graf’s and Dr Milucka’s discovery of this incipient organelle does have an intriguing parallel, for mitochondria are not the only organelles to arrive in eukaryotic cells as bacteria. So-called plastids, found in algae and plants (and which, among other things, permit those organisms to photosynthesise), did so too. And they also turned up twice—the first time about 1.5bn years ago and the second some 60m years in the past.

The search is therefore now on for other novel organelles, perhaps encoding other types of respiration, in other single-celled eukaryotes lurking in obscure parts of the world. The more such examples are found, the better the process of organelle formation will be understood, and with it, that mysterious ancestral organism which eventually gave rise to people.

This article appeared in the Science & technology section of the print edition under the headline “Mitochondria 2.0”