Cell: A new family of mobile genetic elements that allow the horizontal transfer of large genes

From the tropics to the poles, from the surface to a few hundred feet below, the world's oceans are filled with one of the smallest organisms: bacteria called Prochlorococcus, which, despite their small size, are collectively responsible for a significant portion of the ocean's oxygen production
.
But why these small creatures are so diverse and adaptable to such very different environments is a mystery
.

Now, new research shows that these tiny bacteria can exchange genetic information
with each other through a previously undocumented mechanism, even at great distances.
This allows them to transmit an entire piece of gene, such as those that give it the ability to metabolize a particular nutrient or ward off a virus, even in areas where their numbers in water are relatively scarce
.

The findings describe a new class of genetic factors involved in horizontal gene transfer, in which genetic information, whether within the same species or between species, is transmitted directly between organisms through non-direct inheritance
.
The researchers refer to the material that makes this transfer as "tycheposons," which are DNA sequences that can include several complete genes as well as surrounding sequences that can be spontaneously isolated from surrounding DNA
.
They can then be transported to other organisms through one or another possible carrier system, including tiny bubbles called vesicles that cells can create from their own membranes
.

The study included the analysis of hundreds of prochlorococcus genomes from different ecosystems around the world, as well as samples of different variants cultured in the laboratory, and even evolutionary processes
conducted and observed in the laboratory.
The study, published in the journal Cell, was led by former MIT postdocs Thomas Hackl, Sallie "Penny" Chisholm, and Raphaël Laurenceau
.

Chisholm, who played a role in the discovery of these ubiquitous organisms in 1988, said of these new discoveries: "We're very excited about this because it's a new bacteria-level gene transferr that explains many of the patterns we're seeing in wild Prochlorococcus, incredibly diverse
.
" Its tiny variant is now considered the world's most abundant photosynthetic organism and the smallest
of all photosynthetic organisms.

Hackl, now working at the University of Groningen in the Netherlands, said the work began by studying 623 reported genome sequences of different species of Prochlorella from different regions, trying to figure out how they could lose or gain specific functions so easily, despite their apparent lack of any known systems that promote horizontal gene transfer, such as plasmids or viruses
known as probacteriophages.

They studied "islands" of genetic material, which appear to be hotspots of variation, often containing genes involved in known key survival processes, such as the ability to
absorb essential, often restrictive, nutrients such as iron, nitrogen or phosphate.
These silos contain genes that vary greatly from species to species, but they always appear in the same part of the genome, and sometimes even in very different species—a strong indicator of
horizontal shift.

But the genome doesn't show any of the usual traits associated with so-called mobile genetic elements, so initially this remains a mystery
.
Gradually, it was discovered that this system of gene transfer and diversification differed from several other mechanisms
observed in other organisms, including humans.

Hackl describes their findings as a set of genetically similar Lego bricks, with pieces of DNA bundled together
in a way that almost instantly gives the ability to adapt to a particular environment.
For example, a species limited by the availability of a particular nutrient can obtain genes
necessary to enhance the absorption of that nutrient.

These microbes appear to have used a variety of mechanisms to transport these tycheposons (the name comes from the name of the Greek goddess Tyche, the daughter of Oceanus).

One uses membrane vesicles, small bubbles that break off the surface of bacterial cells and release tycheposons
in them.
Another approach is to "hijack" viral or bacteriophage infections and allow them to carry tycheposons and their own infectious particles, called capsids
.
These are effective solutions, Hackl said, "because in the open ocean, these cells have very little cell-to-cell contact, so it is difficult for them to exchange genetic information
without a vector.
" ”

Sure enough, when they studied capsids, or vesicles, collected from the high seas, "they were actually quite abundant" of these genetic elements, Hackl said
.
Useful genetic coding packages "actually swim in these extracellular particles and potentially be taken up
by other cells.
" ”

"In the world of genomics, there are many different types of these elements," such as DNA sequences
that can be transferred from one genome to another.
However, "this is a new type, a unique family
of mobile genetic elements.
" It has similarities to the others, but is not really closely related
to any of them.
”

While the study was specific to Prochlorella, Hackl said the team thinks the phenomenon may be more prevalent
.
They have found similar genetic elements in other, unrelated marine bacteria, but have not yet analyzed the samples in detail
.
"Similar elements have been found in other bacteria, and we now think they may function similarly
," he said.

"It's a plug-and-play mechanism where you can have all kinds of parts and do all kinds of different combinations
.
Due to the huge population size of Prochlorella, it can play a lot and try a lot of different combinations
.
”

Nathan Ahlgren, assistant professor of biology at Clark University who was not involved in the study, said: "The discovery of tycheposons is important and exciting because it provides a new mechanism to understand how Prochlorococcus is able to exchange new genes and thus ecologically important features
.
Tycheposon offers a new explanation
of the mechanism.
They took a creative approach to identifying and characterizing these new genetic elements
that are 'hidden' in the prochlorococcus genome.
”

He added that genome islands, the parts of the genome where these tycheposons were found, "are found in many bacteria, not just marine bacteria, so future research on tycheposons has broader implications
for our understanding of the evolution of bacterial genomes.
" ”