The structure of microbial shuttle genes has existed since ancient times

The earliest life forms on Earth eventually chose one of three different paths, forming the realm of
eukaryotes, bacteria, and archaea.
These regions have evolved over billions of years
.

Recent evidence suggests that the line between these three areas is not so clear
.
Studies have shown that members of different domains can transmit genes back and forth, potentially tracking evolution
quickly.
How they do this is unclear, but a study published today (Nov.
16) in the journal Science Advances, which for the first time reports that archaea have integrons – gene exchange mechanisms
previously thought to only exist in bacteria.
This may allow microbes from both regions to exchange information and immediately acquire new functions
.

Olga Zhaxybayeva, an evolutionary biologist at Dartmouth College who was not involved in the study, said: "We have long known that bacteria and archaea exchange a lot of genes
.
If integrators are widespread in archaea, this could be another mechanism
for microbial exchange of desired characteristics.
”

Gene exchange can help bacteria survive in new, harsh environments or strengthen their symbiotic relationship
with plants.
Study co-author Timothy Ghaly, a microbiologist at Macquarie University in Sydney, said he and his team had been interested in how integrators could give bacteria novel and sometimes incredibly useful properties, such as antibiotic resistance
.

Whether archaea have integrators is unknown, in part because they are difficult to study, Ghaly said, because they live in a variety of hard-to-reach environments, from our guts to muddy sulfur springs
.
But recent advances in genome sequencing, particularly a technique called metagenomic assembled genome (MAG), have allowed researchers to piece together archaeal genomes
from environmental samples.

Ghaly and his team were curious to see if prokaryotes had similar gene exchange mechanisms
to their distant relatives.
If completely different groups of organisms, such as bacteria and archaea, exchange genes, this could help "microbes that accept new functions occupy new niches and may have implications for human and animal and plant health," he added
.
"Integrators are an important enabler of the antibiotic resistance crisis.
.
.
There are a lot of gene boxes that are toxic genes or antibiotic resistance genes that can negatively affect us
.
"For example, some human methanogenic archaea are highly resistant to antibiotics
.

Bacteria exchange genes in the form of gene boxes that consist of
a single gene and a genetic recombination site called AttC.
When they are stressed, the bacteria swap the tapes like mixed tapes, inserting them into or taking out the genome
.

To begin the DNA transfer process, bacteria use integratase (IntI), a protein
in the tyrosine kinase family.
Intl induces recombination
between the AttC site of the gene box and a region on the bacterial genome called the integrator attachment site (AttI).
The genome of a bacterium contains a long string of gene boxes
strung together by AttC sites.

On the bacterial genome, integrons consist of a gene Int of an IntI protein and a series of integrated gene boxes
.
In the new study, the researchers screened all publicly available archaeal genomes, 95 percent of which were MAGs
.
They looked for AttC-like sequences and IntI-like protein-coding sequences
.
The researchers say they haven't found a way to predict AttI sequences, so they haven't looked for them
.

Of the nearly 6,700 original genomes they scanned, the researchers found evidence
of the presence of integrators in 75 across nine gates.
All archaeal integrators have the same structure and composition
as bacterial integrators.

Based on the sequences they found, the researchers synthesized AttC-containing boxes of archaea and found that when E.
coli were exposed, the boxes were incorporated into their
genomes.

"It's always interesting to find (horizontal gene transfer) in new organisms," Zhaxybayeva said
.
She added that in the future, it would be useful to have a complete genome of cultured archaea rather than a constructed MAG like the one the research team used in this study, and to begin piecing together the mechanisms
behind gene transfer.
She is particularly interested in whether archaea in the human gut have integrators, "and whether they are involved in the exchange
of antibiotic resistance.
" ”