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New DNA Degradation-Suppressant Protein Found in Extremotolerant Tardigrade Genome

NEW YORK (GenomeWeb) – A Japanese research team has sequenced the genome of the extremotolerant tardigrade (Ramazzottius varieornatus) — the most stress tolerant species of tardigrade — and has identified a gene responsible for producing proteins that suppress X-ray radiation-derived DNA degradation. The researchers published their findings today in Nature Communications.

Tardigrades are microscopic organisms commonly known as water bears. They are of particular interest to scientists because they can survive in extremely stressful environments, including the vacuum of space. Learning more about their genetic makeup could lead to advances that would help humans better tolerate high-stress environments, such as space.

Researchers published the first sequence of a tardigrade (Hypsibius dujardini) in 2015, which suggested that the animal acquired a significant amount of its genes from other species through horizontal gene transfer. However, a study that came out earlier this year in the Proceedings of the National Academy of Sciences cast doubt on the initial findings.

For this study, the team extracted DNA from starved and well-cleaned R. varieornatus tardigrades. They performed whole genome sequencing and RNA sequencing on Illumina Genome Analyzer IIx and HiSeq2000 sequencers, and Sanger sequencing. The researchers wrote that they were able to "determine a high-quality genome sequence" of the R. varieornatus tardigrade, adding, "All examined data, including congruence of the assembly span with the estimated genome size, and high coverage of [expressed sequence tags] and a core eukaryotic gene set, support the completeness of the determined genome sequence."

To home in on individual gene function, the researchers extracted total RNA from dehydrated tardigrade samples and performed expressed sequence tag sequencing on Applied Biosystems ABI 3730xl capillary sequencers. They mapped the RNA-seq reads to the genome sequence using TopHat software, producing a comprehensive set of protein-coding gene predictions.

In line with the PNAS study that came out earlier this year, the researchers found no evidence of extensive horizontal gene transfer. But they did find that, compared to flies and worms, tardigrades had an increase in genes responsible for the tolerance of stressful environments.

"Some tardigrade-unique genes, including putative protective proteins CAHS and SAHS, were abundantly and constitutively expressed, and could be candidates involved in desiccation tolerance," the researchers wrote.

The researchers also identified a damage suppression protein (Dsup) that binds to DNA, and found that the gene that codes for this protein is likely to be unique to the tardigrade lineage based on a detailed comparison between tardigrade genes and those of other species. "Dsup protein is a prominent example of tardigrade-unique abundant proteins involved in tolerability and is, to our knowledge, the first DNA-associating protein demonstrated to protect DNA and improve the radiotolerance of cultured animal cells," they added.

To understand how this protein affects mammalian cells, the researchers took cells from the HEK293 cell line, treated some with Dsup and left others alone, and irradiated them all. They found that Dsup has a protective effect against the X-rays which would normally induce severe DNA damage.

"Almost all irradiated untransfected cells had an abnormal round shape and were mostly detached from the culture dish, typical characteristics of dead cells," they wrote. "In contrast, many irradiated Dsup-expressing cells had a normal morphology and attached to the culture dishes, suggesting that these cells retained the characteristics of live adherent cells and perhaps even had proliferative ability." 

Further, the team attempted to confirm that the Dsup treated cells could indeed proliferate, examining the change in cell numbers over a period of time. They found that "even under non-irradiated conditions, Dsup-expressing cells proliferated slightly faster than the untransfected cells, whereas Dsup-knockdown cells exhibited similar proliferation to that of untransfected cells." 

While the researchers are still unclear how tardigrades' unique adaptations function at either the molecular or organism level, these results suggest that tardigrades have evolved unique strategies to cope with stressful conditions. Eventually, the researchers hope this could lead to solutions for humans attempting to survive stressful conditions or environments.