Earth’s early lifeforms eventually took on one of three forms paths, forming the domains of Eukarya, Bacteria and Archaea. These domains have been evolving separately for billions of years.
Recent evidence suggests that the boundaries between the three domains are not so clear cut. Studies show that members of different fields can Traffic genes back and forth, which could speed up evolution. How they do this remains unknown, but a study published today (16 November) in Scientists progress provides a possible clue with the first report that archaea have integrons – gene-swapping machinery previously thought to exist only in bacteria. This can allow microbes from both domains to exchange information and instantly acquire new functions.
“We have known for some time that there are many genes that bacteria and archaea exchange,” says Olga Zhaxybayeva, an evolutionary biologist at Dartmouth College who was not involved in the study. If integrons turn out to be widespread in archaea, “this could be another mechanism for microbes to swap the traits they need.”
Gene swapping may help bacteria to survive in harsh new environments, or strengthen their symbiotic relationships with plants. Study co-author Timothée Ghalymicrobiologist at Macquarie University in Sydney, says he and his team have always been interested in how integrons enable bacteria to take on new, sometimes incredibly useful traits, such as antibiotic resistance.
Whether archaea had integrons was unclear, in part because they’re difficult to study, Ghaly says, because they live in a variety of hard-to-reach environments, from our guts to muddy, sulfuric hot springs. But recent advances in genomic sequencing, particularly a technique called metagenome-assembled (MAG) genomes, have allowed researchers to piece together archaeal genomes from environmental samples.
Ghaly and his team were curious whether prokaryotes might have gene-swapping mechanisms similar to their distant bacterial relatives. If very different groups of organisms, such as bacteria and archaea, exchange genes, it could potentially help “the microbe given a new function to occupy a new niche, and could have impacts on human, animal and plant,” he added. “Integrons are a great facilitator in the antibiotic resistance crisis. . . There are many gene cassettes that are virulence genes or antibiotic resistance genes that could affect us negatively. Humans methanogenic archaea are very resistant to antibiotics, for example.
Bacteria exchange genes in the form of a gene cassette consisting of a single gene and a gene recombination site called AttC. When they encounter stressful circumstances, bacteria swap these tapes like mixtapes, plugging them in and out of their genomes.
To start the DNA transfer process, bacteria use integron integrase (IntI), a protein from the tyrosine kinase family. Intl induces recombination between cassette genes AttC site and a region of the bacteria genome called an integron binding site, or AttI. Bacteria are left with a long chain of gene cassettes, strung together by AttC sites, in their genomes.
On the bacterial genome, the integrons consist of a gene for an IntI protein, int, followed by a series of integrated gene cassettes. In the new study, the researchers screened all publicly available archaeal genomes, 95% of which were MAGs. They looked for AttC-like sequences and for sequences encoding IntI-like proteins. Researchers say they haven’t found a way to predict AttI sequences, and therefore did not search for them.
In the roughly 6,700 archaeal genomes they scanned, the researchers found 75, spanning nine phyla, that showed evidence of integrons. All archaeal integrons had the same structure and components as bacterial integrons.
Based on the sequences they found, the researchers then synthesized archaea AttC-containing tapes and found that, when exposed, E.coli bacteria have incorporated these cassettes into their genomes.
“It’s always interesting to find [horizontal gene transfer] into new organisms,” says Zhaxybayeva. She adds that in the future, it would be useful to have a complete genome of a cultured archaea, as opposed to a constructed MAG like the team used in this study, and begin to piece together the mechanism behind it. gene transfer. She is particularly interested in whether archaea in the human gut have integrons, “and whether they participate in the exchange around antibiotic resistance.”