Comparative genomics of mortal and immortal cnidarians unveils novel keys behind rejuvenation

Abstract

Turritopsis dohrnii is the only metazoan able to rejuvenate repeatedly after its medusae reproduce, hinting at biological immortality and challenging our understanding of aging. We present and compare whole-genome assemblies of T. dohrnii and the nonimmortal Turritopsis rubra using automatic and manual annotations, together with the transcriptome of life cycle reversal (LCR) process of T. dohrnii. We have identified variants and expansions of genes associated with replication, DNA repair, telomere maintenance, redox environment, stem cell population, and intercellular communication. Moreover, we have found silencing of polycomb repressive complex 2 targets and activation of pluripotency targets during LCR, which points to these transcription factors as pluripotency inducers in T. dohrnii. Accordingly, we propose these factors as key elements in the ability of T. dohrnii to undergo rejuvenation.

Keywords: Turritopsis; aging; pluripotency; polycomb; reprogramming.

Fig. 1.

Geographical origin and life cycle diagram of T. rubra (Left) and T. dohrnii (Right). Light blue arrows indicate the typical life cycle while dark blue indicates the alternative ontogeny reversal of T. dohrnii. In this process, the free swimming medusa shrinks until the cyst stage, where all structures from the medusa totally disappear into a homogeneous opaque mass. Later, a stolon starts growing from the cyst and polyp buds appear to become fully grown polyps afterward.

Fig. 2.

Genomic basis of longevity in Turritopsis. Genes potentially implicated in cellular plasticity in T. dohrnii (Top) and T. rubra (Bottom) classified according to their putative role in the different hallmarks of aging. * indicates genes with copy number variations, while ^ refers to genes with point variants of interest.

Fig. 3.

Structural and functional comparisons between POT1 from Turritopsis and other species. The figure shows a partial amino acid sequence alignment of POT1 from Turritopsis and other cnidarians, invertebrates and vertebrate species. Significant variants in T. dohrnii and T. rubra are highlighted with a red box and the arrow indicates the specific position. The figure also shows protein structures built with AlphaFold using H. sapiens structure (A) wild-type, (B) with T. rubra, and (C) T. dohrnii variants, and using (D) T. dohrnii and (E) T. rubra wild-types. Dark blue surface indicates oligonucleotide binding fold (OBF) domain which binds to ssDNA and green area represents OB-fold domain and a Holliday junction resolvase (HJR) domain which make dimer contacts with TPP1. Yellow structure is a tentative representation of the telomeric region, located by superimposing POT1-telomere model (PDB ID 1XJV) on each AlphaFold model. (F) Binding of the different POT1 variants to a single-stranded oligonucleotide containing three telomeric repeats. Blue arrows point to POT1-(TTAGGG)₃ complexes (G) Western blot to check the amount of POT1 loaded in the binding assay.

Fig. 4.

Heatmap of pluripotency targets (NANOG, OCT4, SOX2, and MYC targets) (A) and PRC2 targets (B) during LCR of T. dohrnii. The figure also shows the expression of genes potentially inducing pluripotency (Left) and genes coding for the PRC2 components (Right). Note that heatmap “A” only includes targets of pluripotency genes whose expression in any stage from incubation to polyp was clearly different from their expression in medusa and in no reversal stages.