Some Archaea have integrons, allowing gene transfer between domains

Tape Recruitment (attC × atti recombination). (A) Schematic depicting the experimental setup of cassette insertion assays. Kanamycin resistance (Km^R) suicide vector pJP5603 with a attC the site is delivered to the recipient E.coli Strain UB5201 by conjugation. The recipient strain carries a you1 gene, expressed from the inducible P_WRONG promoter, and a attI1 site, residing on resistance to carbenicillin (Cb^R) pBAD24 and chloramphenicol resistance (Cm^R) pACYC184 backbones, respectively. The donor suicide vector cannot replicate in the recipient host and therefore can persist only after attC × atti recombination to form a plasmid co-integrate. (B) Mean recombination frequencies (log_ten scale, ±1 SE) between attI1 and nine archaea attCs (with original forks labeled along the x-axis) and the paradigmatic bacterium attC to place (attC_aadA7), used as a positive control. Mean frequencies were calculated following three independent cassette insertion tests (see Materials and Methods for details). No statistically significant differences in recombination frequencies were detected among the attCs (Kruskal-Wallis test, n=27; df=8, P=0.488). Recombination frequencies are given for attC lower strands only. See Table S1 for attC upper strand recombination frequencies. NS, not significant. Credit: Scientists progress (2022). DOI: 10.1126/sciadv.abq6376

A team of researchers from Macquarie University, Australia, found evidence showing that some Archaea have integrons. In their article published in the journal Scientists progressthe group describes how they used a recently developed technique called metagenome-assembled genomes (MAG) to study the genomes of Archaea samples in a new way, and what they learned while doing so.

Life on Earth is divided into three domains, Eukarya, Bacteria and Archaea. The third domain, Archaea, is similar to bacteria – its members are often called Archaebacteria. Like bacteria, archaea are unicellular but unlike bacteria, they depend on lipids in their cell membranes.

In this new effort, the researchers were examining the means by which bacteria and archaea exchanged genes and wondered if it was possible that they had integrons – systems for capturing and delivering genes in bacteria that use gene cassettes to pass the proteins involved. To find out, they turned to MAG, a technique that searches for single gene and gene recombination sites called AttCs that sequence the coding for the protein integron integrase (IntI).

Using the technique, they found many matches. Out of 6,700 scanned genomes, they found 75 matches, across nine phyla, each showing evidence of an integron. And all of them were found to have the same structure as the integrons found in Bacteria, which suggested the use of cassettes.

The researchers thought this indicated that the archaea they had identified should be able to exchange genes with bacteria and vice versa, just as easily as bacteria exchange genes with each other. To prove that their idea was correct, they synthesized AttC from a specimen of Archaea and exposed it to a specimen of E. coli. The tests showed that cassettes had been created allowing the exchange of genes to occur.

The discovery of integrons in Archaea will certainly open new avenues of research. One of them would be to examine the possibility that the exchange of genes from Archaea to bacteria helps the latter to become resistant to drugs intended to kill them. The researchers also note that it would be helpful if a complete Archaea genome were made available.

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