When a newt loses a leg—or part of its heart or an eye, among other organs—it can replace the missing body part by turning on genes that coax new cells to grow. Knowing how this process works on the molecular level could help treat human disease, but the identities of the genes involved have largely remained a mystery.
In the past, researchers have struggled to identify the newt’s regeneration genes because the animal has an unwieldy genome. “The newt genome is relatively large,” said Thomas Braun of the Max-Planck-Institute for Heart and Lung Research and an author of the new paper published January 20 in Genome Biology (1). “It’s ten times the size of mammalian genomes and that makes it rather difficult, in terms of the bioinformatics required, to do full-scale sequencing.”
So Braun’s team decided to forego gene sequencing, and instead focused on the transcriptome of the newt—the collection of all the RNA molecules in the animal’s cells. Much of the newt’s large genome, they believed, consisted of introns, which are not actively translated into protein. The team assembled a transcriptome with 120,922 non-redundant transcripts, which included transcripts from all stages of regeneration in various organs. Some of those transcripts were similar to those found in other organisms.
But Braun and his colleagues wanted more information on specific proteins involved in regeneration, not just the transcripts, which may not necessarily get translated into proteins. So they isolated proteins from newt tissues—including heart, eye lens, tail, liver, and spleen—during regeneration. They characterized the proteins using mass spectrometry and then compared the protein sequences with the transcripts they found.
“The real highlight of our study is that we brought together two different techniques to study this,” said Braun. “Using both transcriptomics and proteomics allowed us to get a fuller picture.”
The researchers spelled out the details of 55,605 peptides that matched up with 14,471 transcripts from their earlier experiments. More than 10,000 transcripts encoded multiple proteins, and more than 500 peptides have not been identified in any other organisms previously.
“It was indeed a surprise that there are numerous new genes not found in other organisms,” said Braun. “Whether this is directly correlated with regenerative capacity, we don’t know yet.”
For now, the results don’t give an immediate answer to how newts and related animals mediate the regeneration of so any body parts, but instead offer a starting point for scientists who have lacked concrete genetic data on the amphibian. But the successful combination of transcript data with proteome data can now be applied to other animals with difficult genomes.
“There are numerous other organisms with especially large genomes – other amphibians in particular – that this technique could be applied to,” said Braun.
- Looso M, Preussner J, Sousounis K, Bruckskotten M, et. al. A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration. (2013) Genome Biology 14:R16.