Newts, urodelian amphibians as axolotls, show a great regenerative capacity compared to most vertebrates. Similarly to axolotls, that are really paedomorphic retaining larval features, truly adult newts can regenerate limbs, lenses, the heart and CNS neurons, for example. Due to its enormous genome size (about ten times the size of human genome), however, previous attempts to have a sequenced genome or reference transcriptome had not been very successful. But things look very different now as the laboratories of Thomas Braun and his collaborators have just published a de novo assembly of the transcriptome of Notophtalmus viridescens, a newt model species for regeneration (http://www.ncbi.nlm.nih.gov/pubmed/23425577). The authors combined several sequencing approaches and platforms to end up with around 38,000 annotated putative transcripts, from which about 15,000 have been validated, by proteomics, to code for proteins. Total RNA was obtained from a variety of uninjured tissues as well as from regenerating hearts, limbs and tails at different timepoints. Also, RNA was obtained from different developmental stages with the purpose of getting as many transcripts as possible.
One of the most surprising results after the bioinformatic analyses of such amount of data has been the identification of new protein families, some of them urodele-specific and some of them newt-specific. Thus, the authors report 583 protein-coding transcripts with no hit in public databases and 243 protein-coding transcripts similar to urodele proteins only. Expression analyses (by microarrays and RT-PCR) of some of these genes during the regeneration of different organs, such as the heart and lens, show that they display specific expression changes during the regenerative process (either upregulation or downregulation). These results, as the authors discuss, may provide some light over the debate on whether the regenerative capacity has appeared convergently many times in distinct lineages or is in fact a basal feature of metazoans that has been, otherwise, lost in many other lineages. Although it seems clear that newts may have novel protein families the question that needs to be solved next is whether or not these proteic novelties are fundamental for the amazing regenerative capacities of newts compared to other vertebrates, including other amphibians. So, and it has been pointed out in previous comments to some posts of this blog, once the “omics” approach is done it is time then to go back to the real animal and check in vivo the function of all these putative interesting genes. Also, here, it will be fundamental to compare the function of orthologues in different species with similar or different regenerative capacity. For example, the authors show here how some newly identified genes show specific expression changes in dorsal and ventral iris during lens regeneration (by RT-PCR). It could be then interesting to go deeper and characterize the expression of these genes by in situ hybridization during lens regeneration and compare it to, for example, what happens during axolotl lens regeneration. As said in a previous post, whereas newts regenerate their lenses from the dorsal iris, axolotls can regenerate them from both dorsal and ventral iris (only at a specific developmental stage).
Although the idea that species that regenerate can do it because they have a “magical regeneration gene” (not present in non-regenerating animals) can be somehow appealing, the reality is that in most classical models of regeneration there are not really many proved examples yet of these magic species-specific factors. One of these genes, found in newts, is Prod1 that belongs to a family of three-finger protein (TFP) specific to salamanders and that is required for limb regeneration.
But looking at the phylogenetically wide distribution of regeneration as a trait, it seems reasonable also to consider that regeneration is probably an ancestral trait already present at the base of metazoans. That would account for the fact that animals that regenerate share key features for a successful regeneration such as for example a scarless wound healing and the capacity to re-activate conserved molecules and pathways that are only active during embryonic development in those species with poor regenerative capabilities. On the other hand, however, it could be also true, as it may happen in newts, that upon these conserved basic properties different lineages may have incorporated specific elements such as for example Prod1. Thus, in newts Prod1 exerts its function by interacting with other well conserved elements such as nAG or EGFR (epidermal growth factor receptor). In fact Prod1, as well as other TFP members are quite interesting from an evolutionary point if view because not only is Prod1 different in newts and axolotls (GPI-anchored in newts and secreted in axolotls), but also there are other examples of TFPs that appear specific of certain taxons. Another taxon-specific TFPs include some required for the formation of venom apparatus in elapid snakes and a GPI-anchored protein in Drosophila that binds to the shaker potassium channel.
So, maybe in evolutionary terms regeneration is an ancestral trait that in different lineages may have incorporated into its molecular programme taxon-specific elements to promote, trigger or enhance this amazing process. Newts, as suggested by the data presented in this paper, can become an excellent model in which to analyze whether its amazing regenerative abilities depend upon these novel identified proteins and how these interact with well-conserved molecules and pathways that are necessary to be reactivated during regeneration.