Prochlorococcus is the smallest and numerically most abundant cyanobacteria in the oceans. It has a large pan genome and hypervariable genomic islands linked to niche differentiation and phage defense. The smallest and most numerous cyanobacteria in the oceans is Prochlorococcus.
According to recent research from MIT, these microscopic bacteria communicate with each other through a previously unknown mechanism, even when they are far apart. This allows them to pass on entire sets of genes, for example allowing them to assimilate a certain type of diet or to protect themselves against viruses, even in areas where their aquatic population is quite low.
According to the findings, a new class of genetic agents involved in horizontal gene transfer — in which genetic material is transferred directly between animals, whether they are of the same species or not — has been discovered by methods other than linear descent. Tycheposons are DNA sequences that can spontaneously detach from surrounding DNA and, according to scientists, contain several complete genes.
Tycheposons are the agents that carry out this transfer. They can then be delivered to other creatures through various carrier systems, such as the vesicles that cells can make from their membranes.
For the study, scientists studied hundreds of Prochlorococcus genomes from various ecosystems around the world, lab-grown samples of different variants, and even evolutionary processes were performed and observed in the lab.
Institute Professor Sallie “Penny” Chisholm said: “We’re really excited about it because it’s a new horizontal gene transfer agent for bacteria, and it explains a lot of the patterns we see in Prochlorococcus in the wild, the incredible diversity. Now thought to be the world’s most abundant photosynthetic organism, the tiny variants of what are known as cyanobacteria are also the smallest of all photosynthesizers.’
MIT postdocs Thomas Hackl said: “The work began by studying the 623 reported genome sequences of different species of Prochlorococcus from different regions, trying to figure out how they could so easily lose or gain certain functions, despite their apparent lack of any of the known systems that promote / enhance horizontal gene transfer, such as plasmids or viruses known as prophages.”
Scientists examined islands of genetic material that appeared to be hotspots of variability and often contained genes associated with known key survival processes, such as the ability to absorb essential, and often limiting, nutrients such as iron, nitrogen or phosphates.
These islands contained genes that differed greatly between species, but occurred consistently in the same regions of the genome and were occasionally nearly identical even in very different species, providing strong evidence of horizontal transfer.
However, the genomes lacked typical features associated with so-called mobile genetic components, so this initially remained a mystery. The fact that this gene transfer and diversity system differed from the many other mechanisms observed in other creatures, including humans, gradually became apparent.
When DNA fragments were bundled together in a way that could almost instantly give the ability to adapt to a given environment, Hackl compares what they discovered to a genetic LEGO set. For example, a species limited by the availability of a particular nutrient can acquire the genes necessary to improve the uptake of that nutrient.
Hackl says, “The microbes seem to use different mechanisms to transport these tycheposons (a name derived from the Greek goddess Tyche, daughter of Oceanus). One is the use of membrane vesicles, which are small bubbles that are removed from the surface of a bacterial cell and released with tycheposons inside. Another is by “hijacking” virus or phage infections and making them carry the tycheposons with their infectious particles called capsids. These are efficient solutions because these cells in the open ocean rarely have cell-to-cell contacts, so it is difficult for them to exchange genetic information without a vehicle.”
And indeed, when capsids or vesicles collected from the open ocean were studied, they “are quite enriched” in these genetic elements. The packets of useful genetic coding “actually swim around in these extracellular particles and may be able to pass through other cells.” be included.”
Chisholm says so “In the world of genomics, there are many different types of these elements” – DNA sequences that can be transferred from one genome to another. However, “This is a new type,” she says. Hackl adds that “It’s a separate family of mobile genetic elements. It has similarities to others, but no close ties to any of them.”
While this study was specific to Prochlorococcus, Hackl says the team believes the phenomenon is more general. They have found similar genetic elements in other, unrelated marine bacteria, but have not yet analyzed these samples in detail. Other bacteria have described similar elements, and we now believe they may work in the same way.”
“It’s a plug-and-play mechanism, where you can have pieces you can play with and make all these different combinations. And with the huge population size of Prochlorococcus, he can play a lot and try many different combinations.”
Nathan Ahlgren, an assistant professor of biology at Clark University who was not involved in this research, says: “The discovery of tycheposons is important and exciting because it provides a new mechanistic understanding of how Prochlorococcus can swap in and exchange new genes, and thus ecologically important traits. Tycheposons offer a new mechanistic explanation for how it works. They found a creative way to fish out and characterize these new genetic elements hiding in the genome of Prochlorococcus.”
- Thomas Hack, Raphael Laurenceau, et al. Novel integrative elements and genomic plasticity in ocean ecosystems. Cell. DOI: 10.1016/j.cell.2022.12.006