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SUNDAY SCIENCE: SCIENTISTS DISCOVER FIRST NITROGEN-FIXING ORGANELLE
 
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Erin Malsbury
April 11, 2024
University California Santa Cruz
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_ After years of work, an international team of scientists have
detected a sign of a major life event that may have only occurred
three times before in the last billion years. They’ve observed two
lifeforms merging into one organism. _

A light microscopy image shows the marine haptophyte algae
Braarudosphaera bigelowii with a black arrow pointing to the
nitroplast organelle, Tyler Coale

 

Modern biology textbooks assert that only bacteria can take nitrogen
from the atmosphere and convert it into a form that is usable for
life. Plants that fix nitrogen, such as legumes, do so by harboring
symbiotic bacteria in root nodules. But a recent discovery upends that
rule. 

In two recent papers, an international team of scientists describe the
first known nitrogen-fixing organelle within a eukaryotic cell. The
organelle is the fourth example in history of primary endosymbiosis
— the process by which a prokaryotic cell is engulfed by a
eukaryotic cell and evolves beyond symbiosis into an organelle.

“It’s very rare that organelles arise from these types of
things,” said Tyler Coale, a postdoctoral scholar at UC Santa Cruz
and first author on one of two recent papers. “The first time we
think it happened, it gave rise to all complex life. Everything more
complicated than a bacterial cell owes its existence to that event,”
he said, referring to the origins of the mitochondria. “A billion
years ago or so, it happened again with the chloroplast, and that gave
us plants,” Coale said. 

The UC Santa Cruz research team, from left to right: Esther Mak,
Jonathan Zehr, Kendra Turk-Kubo and Tyler Coale

The third known instance involves a microbe similar to a chloroplast.
The newest discovery is the first example of a nitrogen-fixing
organelle, which the researchers are calling a nitroplast.

A soft x-ray tomography image shows B. bigelowii cell division, with
the nitroplasts (UCYN-A) in cyan. (Photo credit: Valentina Loconte)

A decades-long mystery

The discovery of the organelle involved a bit of luck and decades of
work. In 1998, Jonathan Zehr, a UC Santa Cruz distinguished professor
of marine sciences, found a short DNA sequence of what appeared to be
from an unknown nitrogen-fixing cyanobacterium in Pacific Ocean
seawater. Zehr and colleagues spent years studying the mystery
organism, which they called UCYN-A. 

At the same time, Kyoko Hagino, a paleontologist at Kochi University
in Japan, was painstakingly trying to culture a marine alga. It turned
out to be the host organism for UCYN-A. It took her over 300 sampling
expeditions and more than a decade, but Hagino eventually successfully
grew the alga in culture, allowing other researchers to begin studying
UCYN-A and its marine alga host together in the lab.

For years, the scientists considered UCYN-A an endosymbiont that was
closely associated with an alga. But the two recent papers suggest
that UCYN-A has co-evolved with its host past symbiosis and now fits
criteria for an organelle.

Organelle origins

In a paper published in Cell
[[link removed](24)00182-X.pdf] in March,
Zehr and colleagues from the Massachusetts Institute of Technology,
Institut de Ciències del Mar in Barcelona and the University of Rhode
Island show that the size ratio between UCYN-A and their algal hosts
is similar across different species of the marine haptophyte
algae _Braarudosphaera bigelowii_.

The researchers use a model to demonstrate that the growth of the host
cell and UCYN-A are controlled by the exchange of nutrients. Their
metabolisms are linked. This synchronization in growth rates led the
researchers to call UCYN-A “organelle-like.” 

“That's exactly what happens with organelles,” said Zehr. “If
you look at the mitochondria and the chloroplast, it’s the same
thing: they scale with the cell.”

But the scientists did not confidently call UCYN-A an organelle until
confirming other lines of evidence. In the cover article of the
journal Science [[link removed]],
published today, Zehr, Coale, Kendra Turk-Kubo and Wing Kwan Esther
Mak from UC Santa Cruz, and collaborators from the University of
California, San Francisco, the Lawrence Berkeley National Laboratory,
National Taiwan Ocean University, and Kochi University in Japan show
that UCYN-A imports proteins from its host cells.

“That’s one of the hallmarks of something moving from an
endosymbiont to an organelle,” said Zehr. “They start throwing
away pieces of DNA, and their genomes get smaller and smaller, and
they start depending on the mother cell for those gene products — or
the protein itself — to be transported into the cell.”

Tyler Coale worked on the proteomics for the study. He compared the
proteins found within isolated UCYN-A with those found in the entire
algal host cell. He found that the host cell makes proteins and labels
them with a specific amino acid sequence, which tells the cell to send
them to the nitroplast. The nitroplast then imports the proteins and
uses them. Coale identified the function of some of the proteins, and
they fill gaps in certain pathways within UCYN-A.

“It’s kind of like this magical jigsaw puzzle that actually fits
together and works,” said Zehr.

In the same paper, researchers from UCSF show that UCYN-A replicates
in synchrony with the alga cell and is inherited like other
organelles. 

Changing perspectives

These independent lines of evidence leave little doubt that UCYN-A has
surpassed the role of a symbiont. And while mitochondria and
chloroplasts evolved billions of years ago, the nitroplast appears to
have evolved about 100 million years ago, providing scientists with a
new, more recent perspective on organellogenesis.

The organelle also provides insight into ocean ecosystems. All
organisms need nitrogen in a biologically usable form, and UCYN-A is
globally important for its ability to fix nitrogen from the
atmosphere. Researchers have found it everywhere from the tropics to
the Arctic Ocean, and it fixes a significant amount of nitrogen.

“It’s not just another player,” said Zehr.

The discovery also has the potential to change agriculture. The
ability to synthesize ammonia fertilizers from atmospheric nitrogen
allowed agriculture — and the world population — to take off in
the early 20th century. Known as the Haber-Bosch process, it makes
possible about 50% of the world’s food production. It also creates
enormous amounts of carbon dioxide: about 1.4% of global emissions
come from the process. For decades, researchers have tried to figure
out a way to incorporate natural nitrogen fixation into agriculture.

“This system is a new perspective on nitrogen fixation, and it might
provide clues into how such an organelle could be engineered into crop
plants,” said Coale. 

But plenty of questions about UCYN-A and its algal host remain
unanswered. The researchers plan to delve deeper into how UCYN-A and
the alga operate and study different strains. 

Kendra Turk-Kubo, an assistant professor at UC Santa Cruz, will
continue the research in her new lab. Zehr expects scientists will
find other organisms with evolutionary stories similar to UCYN-A, but
as the first of its kind, this discovery is one for the textbooks.

_ERIN MALSBURY is a science communication master's student at the
University of California, Santa Cruz. She studied ecology and
anthropology at the University of Georgia and has published work in
Eos , Mongabay , and The Mercury News , among others._

_Known for impactful research, teaching, and public service, UC SANTA
CRUZ leads at the intersection of innovation, social justice, and
sustainability. UC Santa Cruz has been at the forefront
of: Sequencing the human genome, Creating the organic farming
movement,  Unlocking the mysteries of our galaxy, Challenging systems
of oppression to create a more just and equitable society._

The Secret to the Strongest Force in the Universe
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By Stanley J. Brodsky, Alexandre Deur & Craig D. Roberts
Scientific American
New discoveries demystify the bizarre force that binds atomic nuclei
together
April 16, 2024

* Science
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* Evolution
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* prokaryotic cell
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* eukaryotic cell
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* organelle
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