Beyond Endosymbiosis: Discovering the First Nitroplast

June 20, 2024

Cells are often depicted as tiny factories, taking in raw materials and using them to produce what they need to survive. One functionality that was thought to have evaded eukaryotic cells was the ability to suck up nitrogen gas, N2, from the air and convert it into essential amino acids. Until recently, this was a metabolic pathway exclusive to bacteria. However, the discovery of the first nitrogen-fixing organelle (nitroplast)—a structure thought to have been born from the engulfment and evolution of a bacterial cell—is sparking researchers to identify and eventually engineer possible applications, with a particular focus on plant and crop growth.

The Benefits of Endosymbiosis Are Mutual

Endosymbiosis is defined as a mutually beneficial relationship between organisms where one lives inside the other, though it can occur on many scales—not only cells within cells, but also organisms within organisms. Intracellular endosymbionts, in particular, can be important for major evolutionary leaps, such as the evolution of eukaryotic cells. One of the most well-known endosymbiont theories provides an explanation for the evolution of the mitochondria, the powerhouse of eukaryotic cells. Here, the theory is that an archaeal cell engulfed a bacterial cell, which over time evolved from an endosymbiont into the organelle that produces energy through oxidative phosphorylation and regulates metabolic activity of eukaryotic cells.

An endosymbiotic partnership can persist over many generations, sometimes leading to the loss of the endosymbiont's ability to survive outside its host. Such obligate endosymbiosis often develops because of extensive gene loss in key metabolic pathways, leading endosymbionts to become entirely reliant on their hosts for certain nutrients. This is thought to have happened in the example above, as bacterial endosymbionts evolved into the mitochondria organelles they are today.

Illustration of Endosymbiosis theory.
Endosymbiosis is one of the ways in which modern eukaryotic cells could have evolved from prokaryotic ancestors.
Source: Wikimedia Commons.

Successful integration as an endosymbiont, however, does not guarantee evolution into an organelle. What distinguishes an endosymbiont from an organelle is where most of its proteins come from. Endosymbionts encode all of their functional proteins within their own genomes, while organelle proteins are largely encoded in the host's nuclear DNA and transported to the organelle following translation. For example, the bacterial cell that became the mitochondrion is thought to have lost most of its genetic material to the host's nucleus, thus making life outside the host nearly impossible.

Eukaryotes: Now Fixing Nitrogen

From extensive intracellular compartmentalization to forming complex multicellular structures, eukaryotic organisms are incredibly multifaceted and successful. However, until recently, one metabolic function that was thought to have eluded eukaryotes was the ability to take up nitrogen (N2) from the air and use it to produce essential compounds like amino acids. An international team of researchers recently discovered that Braarudosphaera bigelowii, a eukaryotic marine alga, fixes N2 with the help of an N2-fixing organelle that originated from an ancient endosymbiosis with an N2-fixing bacterial cell. The existence of an N2-fixing organelle had been hypothesized, but this is the first evidence for such an organelle occurring in nature.

In the late 1990s, scientists observed a DNA sequence in seawater that seemed to come from an unknown N2-fixing cyanobacterium. They called this then-unculturable organism Candidatus Atelocyanobacterium thalassa, or UCYN-A. After years of work, scientists came to consider it an endosymbiont of B. bigelowii and its close relatives. In classic endosymbiont fashion, UCYN-A has a reduced genome and lacks several major metabolic pathways, such as the tricarboxylic acid cycle that is used to generate energy and molecules to build up biomass.

Illustration of the global presence of UCYN-A.
UCYN-A is globally distributed.
Source: Wikimedia Commons.

Reaping the rewards of figuring out how to grow UCYN-A in the lab, the researchers were able to study the organism in more detail. UCYN-A and B. bigelowii cells appear to be intricately linked—their growth depends on mutual exchange of nutrients, and their growth rates are synchronized. Their cell sizes are also linked, and scale linearly—larger B. bigelowii cells have larger UCYN-A inside them. This led researchers to call UCYN-A a "hypothetical N2-fixing organelle."

A <i>B. bigelowii</i> cell.
A B. bigelowii cell, with the nitroplast highlighted by the black arrowhead.
Source: Wikimedia Commons.
Excitingly, UCYN-A received a status upgrade in April 2024, when an international team of scientists showed that it imports proteins from B. bigelowii cells, a hallmark of organelle status. The researchers isolated UCYN-A from inside the algal cells and compared the amounts of different proteins in the algal cells and isolated UCYN-A. They found that over 350 proteins encoded in B. bigelowii's genome were more abundant in UCYN-A than the alga itself. These imported proteins included enzymes for producing certain amino acids and nucleotides, for which UCYN-A lacks complete pathways and, therefore, cannot produce independently.

New evidence demands new monikers: with this new evidence of protein transport, UCYN-A has gained the status of "early evolutionary stage N2-fixing organelle," also called a nitroplast. With this discovery come exciting new ideas about what the nitroplast enables. For example, one of the main nutrients that plants require is nitrogen, which is often supplemented by ammonia fertilizers that can have negative impacts on the environment. Perhaps future crops can be engineered to take up N2 directly from the air instead, reducing the need for fertilizers.

Out Of the Ocean and Onto Land

With major discoveries such as the nitroplast, it becomes clear how much we have left to learn about the world around us. It is also a reminder of how incrementally science can move, and that groundbreaking discoveries take time. The discovery of the nitroplast started with an interesting observation over 25 years ago and required the work of countless scientists through the years to develop this exciting new discovery. This work will continue as scientists work out how the nitroplast functions, and whether it can be engineered or transferred to other organisms. These ideas might still be a long way from becoming reality, but they demonstrate how much a small former cyanobacterium can teach us.

Interested in learning more about symbiotic relationships amongst microbes and marine animals? Check out this next article from our Spring 2022 issue of our flagship member magazine, Microcosm. The theme of the Spring 2022 issue is Water Microbiology: Bringing Microbes to the surface and is now open to the public. 

Author: Vilhelmiina Haavisto

Vilhelmiina Haavisto
Vilhelmiina Haavisto is a Ph.D. student at ETH Zürich in Switzerland, where she works with marine microbial communities.