November 9th, 2015
Newts and salamanders are known for their ability to re-grow new limbs after injury. But nobody quite understood how they do it. A new study led by researchers at the Max Planck Institute in Germany and the University of Dayton (Ohio) is a significant step towards that understanding, and could help devise ways for non-amphibian species (like us) to regenerate limbs or organs.
Panagiotis Tsonis, Thilo Borchardt, and Thomas Braun led a team that mapped out all of the RNAs (ribonucleic acids) that end up producing proteins unique to salamanders and newts. These RNAs, collectively known as the “transcriptome,” take genetic coding information from DNA and translate that information into working proteins. The group found 826 proteins that are unique to these organisms, and published its results in the Feb. 20 issue of Genome Biology.
One of the obstacles facing the researchers is the lack of complete information about the salamander and newt genome. For a species that has a fully sequenced genome, it’s relatively simpler to identify which of the known genes code for RNA, and then work “downstream” until the proteins are found. But the genomes for these amphibians (known as urodeles) are unusually large (about 10 times the size of the human genome), and have not yet been sequenced. In addition, no “reference genome,” a sequence that is closely related to the amphibians, was available. Without knowing DNA sequences, the scientists then were forced to link RNAs from scratch.
Which is what they did. Working with the red spotted newt, an animal that appears particularly adept at regenerating limbs, hearts and other organs when damaged, they created a new assembly of RNAs from adult and larval animals. They took samples from larval and embryonic organs and undamaged tissues and determined the proteins that were produced. Out of more than 120,000 unique RNAs, they whittled down to the 826 proteins that are found only in newts. Since newts are one of the only species capable of regeneration of tissue, these proteins must somehow regulate that process, the scientists reasoned.
By knowing how these unique proteins are coded, researchers can now determine what genes are responsible for their existence, and how they are regulated. One key question in regeneration is: is this a purely embryonic process, or do adults use other genetic and physiological mechanisms? By pointing at the right genes, we will be able to find an answer and possibly open the door to regeneration in other species.
Source: Genome Biology
Looso, M., et al. (2013). A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration Genome Biology, 14 (2) DOI: 10.1186/gb-2013-14-2-r16
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