Eureka moment with a eukaryote
Certain unicellular organisms have fabulous abilities to create intricate skeletons. How do they do it? The single-cell radiolarian on this grainy photo has provided scientists with an answer to a question that has baffled biologists for over 150 years.
Evolutionary Biologist Anders Krabberød was starting to lose hope.
He had sat for hours with an eye to the microscope. Hundreds of immensely enlarged plankton have slowly drifted past the viewer into their micro cosmos.
Delightful little things, these radiolarians. With their diversity of cytoskeletons and shapes many look like tiny jewellery boxes, or simply jewels. But none match the special type Krabberød is scouting for. Time passes. Some encouragement can be found in Peter Gabriel and Kate Bush. They keep singing “Don’t give up… ”.
Then it happens.
Something glides into view. Krabberød stares. Assesses what he sees.
Yes! Here it is! A teensy-weensy unicellular creature he and his colleagues have been looking for. Krabberød has finally found one, just one specimen.
He carefully sucks the little cell up with a narrow glass straw.
Now, for heaven’s sake, nothing must go awry in the gene sequencing!
Only one cell
Krabberød and some of his colleagues explain to ScienceNordic’s Norwegian partner forskning.no that the little plankton, the radiolarian Sticholonche zanclea, thrives in oceans and of course in Norwegian seawater too, but it cannot be cultivated in a laboratory. Actually, some time has passed since the “Eureka” moment involving a eukaryotic cytoskeleton. But the scientific impact of this little catch has now started to become evident.
Contrary to certain other single-celled creatures, Sticholonche will not reproduce itself in captivity. The researchers had just this one.
That posed a problem.
Normally a whole lot of individual specimens are used when the genes of a unicellular organism are being studied. Millions raised in the lab can be used.
But 80 to 90 percent of unicellular organisms on our planet are like Sticholonche. They don’t thrive in captivity, away from their natural environment and they will not divide and mature. This has hampered studies of their gene functions.
They can be viewed in a microscope, dead or alive, and descriptions can be made of how the live ones behave. But that does not tell scientists which genes link to which characteristics, or enough about how they have evolved.
This is rather irritating when biologists are fascinated by organisms with completely special characteristics, such as the intricate cytoskeleton of Sticholonche and its relatives.
A cytoskeleton is a structure of filaments and microtubules in a cell that give it form, structure and organisation.
The cytoskeleton of Sticholonche and related organisms is much more intricate and complex than in other cells and single-celled creatures.
“The characteristic shapes have fascinated scientists for well over a century. But no one has understood the genetic background for the shapes,” explains Kamran Shalchian-Tabrizi, who headed up the research team Morphoplex at the University of Oslo.
He queries: “Has Sticholonche developed new types of genes or has it changed the way it uses its genes?”
The answer is found in the DNA of these tiny organisms, and especially in their RNA.
What is in use
RNA is like a copy of parts of DNA. When a gene in a strand of DNA is in use, a cell creates an RNA copy of this particular sequence. The copy is sent to other parts of the cell, which use it as a kind of recipe or template conveying genetic information for production of specific proteins.
By charting the RNA copies researchers can detect not only which genes an organism has, but also which ones are actually in use. The RNA of Sticholonche will reveal which genes it uses to construct its special skeleton.
Scientists had not seen the RNA of these unicellular organisms.
But recently they eyed a chance.
“Now the techniques for analysing RNA have become more sensitive, allowing us to study the RNA in just one cell,” says Shalchian-Tabrizi.
“These techniques were developed for lab mice and humans. But we wanted to study all types of single-celled organisms – which, after all, comprise the greatest biodiversity on Earth.”
Shalchian-Tabrizi put together a team of researchers from several disciplines, including biochemistry, genetics, bioinformatics and palaeontology to create a technique that would work for unicellular critters such as Sticholonche.
This was no easy task. One problem is the breaking into this organism’s DNA and RNA.
The group that Sticholonche belong to – Radiolarians – have their famous intricate mineral cytoskeletons. In addition, their DNA and RNA are well protected by special, robust membranes. So how does one crush this cage without messing up the delicate double helix strands of DNA simultaneously?
That is not the only problem. Radiolarians have symbiotic tenants – or partners – symbionts. Algae live inside these unicellular organisms and these partake in photosynthesis. They act as a kind of vegetable garden that produces energy for the radiolarian. These algae have their own DNA and RNA.
Any heavy-handed attempt at charting the genome of a radiolarian will be confounded by bits of DNA and RNA from its “vegetables”.
“As you might guess, we faced lots of challenges,” says Russell Orr, one of the researchers at Morphoplex.
The research team made headway through trial and error. After a few years they arrived at a method. They could then analyse the genetic material of one single-celled organism. Not always, but at least in some of their attempts.
But the question lingered: Could they succeed in analysing the RNA of their single, precious specimen of Sticholonche, which Krabberød had spent so long at the microscope searching for?
Fortunately, it worked.
Thus, the researchers could finally analyse the genetic machinery of the organism to see how it creates its characteristic cytoskeleton.
A surprise was waiting in there.
Several building blocks
When living creatures attain new characteristics they have to get genes which one way or another do something different. How do they do it?
“Studies of plants and animals show that new types or traits usually occur because genes which were already present are regulated and used in a new way,” says Jon Bråte, another of the Morphoplex researchers.
But this is not what happened with Sticholonche.
At some point in evolutionary history the forerunner of Sticholonche made a copy of the genes that architect and build its skeleton. These copies differed from the original and had new characteristics.
So to this day Sticholonche has both the old and the new set of genes, and thus twice as many building blocks for making its skeleton.
“No other groups have copied genes in this way and this explains why radiolarians have such a unique cytoskeleton,” says Shalchian-Tabrizi.
Weighty issue in biology
This one specimen of Sticholonche has now given biologists worldwide the answer to a question that has been asked for nearly 160 years, ever since the German biologist Ernst Haeckel made his famous drawings of radiolarians and their intricate skeletons.
Eventually, studies of more specimens will hopefully duplicate and confirm the findings of the Morphoplex researchers.
Shalchian-Tabrizi explains that the discovery extends beyond these tiny organisms in the oceans.
“One of the cornerstones of biology is to understand the relationship between genes and physical characteristics,” he says.
“Although our goal has been to use RNA from Sticholonche to explain the evolution of the radiolarian cytoskeleton, an overall objective of our research is to gain insights into the general mechanisms that explain complex structures in all types of cells.”
Translated by: Glenn Ostling
- A. K. Krabberød et.al: Single cell transcriptomics, mega-phylogeny and the genetic basis of morphological innovations in Rhizaria, Molecular Biology and Evolution, July 2017.