Evolutionary perspectives of telomerase RNA structure and function

Abstract

Telomerase is the eukaryotic solution to the 'end-replication problem' of linear chromosomes by synthesising the highly repetitive DNA constituent of telomeres, the nucleoprotein cap that protects chromosome termini. Functioning as a ribonucleoprotein (RNP) enzyme, telomerase is minimally composed of the highly conserved catalytic telomerase reverse transcriptase (TERT) and essential telomerase RNA (TR) component. Beyond merely providing the template for telomeric DNA synthesis, TR is an innate telomerase component and directly facilitates enzymatic function. TR accomplishes this by having evolved structural elements for stable assembly with the TERT protein and the regulation of the telomerase catalytic cycle. Despite its prominence and prevalence, TR has profoundly diverged in length, sequence, and biogenesis pathway among distinct evolutionary lineages. This diversity has generated numerous structural and mechanistic solutions for ensuring proper RNP formation and high fidelity telomeric DNA synthesis. Telomerase provides unique insights into RNA and protein coevolution within RNP enzymes.

Keywords: DNA replication; end-replication problem; evolution; polymerase; ribonucleoprotein; telomerase; telomere.

Figure 1.

Phylogenetic relationship and structural domains of TERT and conventional RTs. (Left) The TERT protein is closely related to the RTs from PLEs and non-LTR retrotransposons, which similarly employ target-priming reverse transcription. The phylogenetic tree is based on the shared motifs of the RT domain with bacterial retrons and retrointrons as the outgroup for eukaryotic retrotransposons. (Right) Domain organization of retron, retrointron and retrotransposon RTs. The central catalytic RT domain (red) is flanked by variable accessory domains, including endonuclease (EN, violet), integrase (INT, indigo), RNase-H (RH, pink), RNA binding domain (RBD, blue), and a thumb domain (orange). TERT contains a large N-terminal extension compromising of the DNA binding TEN (green) domain and TR binding domain (TRBD, blue).

Figure 2.

A model for the origin of the telomerase RNP. (A) Telomerase likely originated from an ancient retrotransposon RT that lost its endonuclease domain and associated with a non-coding RNA transcribed from a separate gene. (B) The ancient TR contains a specialized template with the 5′ boundary defined by a TBE (blue). (C) Toward becoming an integral component of the telomerase enzyme, this proto-TR would have evolved a primitive pseudoknot (green) as found in protozoan TRs and a protein-binding structural element (red) for RNP assembly and activity stimulation, which is present in all known modern TRs. (D) TR evolution in fungal and metazoan lineages accompanied the development of a more complex pseudoknot (green).

Figure 3.

Evolution of telomeric DNA repeat and TR template sequences. (Left) Simplified phylogenetic tree of eukaryotic lineages. Branch length does not reflect evolutionary distance. (Right) The TR template is composed of the 3′ alignment (orange) and 5′ templating (green) regions. The alignment region positions the 3′-end of the target DNA through base-pairing interactions, while the templating region specifies the DNA sequence synthesized. Budding and fission yeast TR templates are degenerate, with the alignment and templating regions poorly defined (open box). The 5′-TTAGGG-3′ (blue) telomeric DNA repeat is evolutionary conserved and found in most groups of eukaryotes including early branching flagellates. Deviations from the putatively ancestral telomeric DNA repeat sequence are denoted (black). Telomerases from different species synthesize different permuted registers of the TTAGGG sequence. Representative species shown include Trypanosoma brucei, Tetrahymena thermophila, Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Saitoella complicata, Neurospora crassa, Strongylocentrotus purpuratus, Mus musculus, and Homo sapiens.

Figure 4.

TR domains essential for telomerase enzymatic activity. (A) Within all TRs is the template core domain (red box) with the TBE (blue) and later branching species include an essential pseudoknot structure (PK). The percentage of activity generated by the template core, without the remainder of the RNA is denoted. TR in most species is transcribed by RNA pol II, with a specific and unique transition event to RNA pol III (orange) within the ciliate lineage. The shared CR4/5 (green) among the evolutionarily distant vertebrate and fungal lineages implies a common ancestor with the CR4/5 element. The echinoderm eCR4/5 (green) lacks the P6.1 stem-loop and its presence is less essential for function, while the S. cerevisiae TWJ (black) lacks the P6.1 stem-loop and is not required for function, demonstrating more outlier features from the presumed common TR ancestor (green line). Ciliate helix IV has potentially arisen from convergent evolution (orange). (B) RNA binding motifs in the TERT protein. Schematic of the TERT protein from vertebrates and ciliates denoting the 4 structural domains, TEN, TRBD, RT and C-terminal extension (CTE). Within the TRBD, the TFLY and CP2 motifs (blue) bind TBE, while the CP and QFP motifs (green) associate with CR4/5. Association of ciliate helix IV with TRBD motifs (orange) is speculative.

Figure 5.

Divergent biogenesis pathways for TR maturation. Four mutually exclusive RNA biogenesis pathways, box C/D snoRNA, pol III transcribed small RNA, snRNA, and box H/ACA sno/scaRNA, are employed for TR biogenesis in separate evolutionary lineages. Schematic of the 3′-end biogenesis domains in TRs with important recognition motifs denoted (colored boxes). The wide array of distinctive 3′-end processing mechanisms is listed. TR associated proteins listed have been determined to directly bind to TR. Mechanisms and accessory proteins that have not been determined (N.D.) as well as telomerase and telomere accessory proteins that do not directly bind to TR are omitted.